146 lines
4.2 KiB
Java
146 lines
4.2 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.ArrayList;
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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.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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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 com.fasterxml.jackson.databind.ObjectMapper;
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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.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import scala.Tuple2;
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public class SparkCountryPropagationJob3 {
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private static final Logger log = LoggerFactory.getLogger(SparkCountryPropagationJob3.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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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SparkCountryPropagationJob3.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 inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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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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final Boolean saveGraph = Optional
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.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("saveGraph: {}", saveGraph);
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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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execPropagation(
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spark,
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inputPath,
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outputPath,
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resultClazz,
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saveGraph);
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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 inputPath,
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String outputPath,
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Class<R> resultClazz,
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boolean saveGraph) {
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if (saveGraph) {
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// updateResultTable(spark, potentialUpdates, inputPath, resultClazz, outputPath);
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log.info("Reading Graph table from: {}", inputPath);
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaPairRDD<String, R> results = sc
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.textFile(inputPath)
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.map(r -> OBJECT_MAPPER.readValue(r, resultClazz))
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.mapToPair(r -> new Tuple2<>(r.getId(), r));
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JavaPairRDD<String, R> tmp = results.reduceByKey((r1, r2) -> {
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if (r1 == null) {
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return r2;
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}
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if (r2 == null) {
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return r1;
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}
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if (Optional.ofNullable(r1.getCollectedfrom()).isPresent()) {
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r1.setCountry(getUnionCountries(r1.getCountry(), r2.getCountry()));
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return r1;
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}
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if (Optional.ofNullable(r2.getCollectedfrom()).isPresent()) {
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r2.setCountry(getUnionCountries(r1.getCountry(), r2.getCountry()));
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return r2;
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}
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r1.setCountry(getUnionCountries(r1.getCountry(), r2.getCountry()));
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return r1;
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});
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tmp
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.map(c -> c._2())
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.map(r -> OBJECT_MAPPER.writeValueAsString(r))
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.saveAsTextFile(outputPath, GzipCodec.class);
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}
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}
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private static List<Country> getUnionCountries(List<Country> country, List<Country> country1) {
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HashSet<String> countries = country
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.stream()
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.map(c -> c.getClassid())
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.collect(Collectors.toCollection(HashSet::new));
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country
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.addAll(
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country1
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.stream()
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.filter(c -> !(countries.contains(c.getClassid())))
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.collect(Collectors.toList()));
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return country;
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}
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}
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