selection of the results id having the given country among the countries, or being in relation with other entities associated with the given country
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package eu.dnetlib.dhp.oa.graph.dump.country;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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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.FilterFunction;
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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.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.Node;
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import org.dom4j.io.SAXReader;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.xml.sax.SAXException;
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import scala.Tuple2;
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import java.io.Serializable;
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import java.io.StringReader;
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import java.util.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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/**
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* @author miriam.baglioni
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* @Date 27/04/23
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* Finds the results id which are in relation with another entity having the given country
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* or that have that country in the country list
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*/
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public class SparkFindResultsRelatedToCountry implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkFindResultsRelatedToCountry.class);
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public static final String COMPRESSION = "compression";
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public static final String GZIP = "gzip";
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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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SparkFindResultsRelatedToCountry.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/input_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 = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final 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 country = parser.get("country");
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run(
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isSparkSessionManaged, inputPath, outputPath, country);
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}
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private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath,
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String country) {
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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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findRelatedEntities(
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spark, inputPath, outputPath, country);
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});
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}
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public static <I extends eu.dnetlib.dhp.schema.oaf.Result> void findRelatedEntities(
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SparkSession spark,
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String inputPath,
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String outputPath,
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String country) {
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Dataset<Project> projectsInCountry = Utils.readPath(spark, inputPath + "/project", Project.class)
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.filter((FilterFunction<Project>) p -> isCountryInFunderJurisdiction(p.getFundingtree(), country));
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Dataset<Relation> relsProjectResults = Utils.readPath(spark, inputPath + "/relation", Relation.class)
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.filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
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r.getRelClass().equals(ModelConstants.PRODUCES));
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projectsInCountry.joinWith(relsProjectResults, projectsInCountry.col("id").equalTo(relsProjectResults.col("source")))
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.map((MapFunction<Tuple2<Project, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
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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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Dataset<Organization> organizationsInCountry = Utils.readPath(spark, inputPath + "/organization", Organization.class)
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.filter((FilterFunction<Organization>) o -> o.getCountry().getClassid().equals(country));
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Dataset<Relation> relsOrganizationResults = Utils.readPath(spark, inputPath + "/relation", Relation.class)
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.filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
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r.getRelClass().equals(ModelConstants.IS_AUTHOR_INSTITUTION_OF));
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organizationsInCountry.joinWith(relsOrganizationResults, organizationsInCountry.col("id").equalTo(relsOrganizationResults.col("source")))
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.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
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.write()
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.option(COMPRESSION, GZIP)
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.mode(SaveMode.Append)
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.json(outputPath );
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selectResultWithCountry(spark, inputPath, outputPath, country, "publication", Publication.class);
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selectResultWithCountry(spark, inputPath, outputPath, country, "dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
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selectResultWithCountry(spark, inputPath, outputPath, country, "software", Software.class);
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selectResultWithCountry(spark, inputPath, outputPath, country, "otherresearchproduct", OtherResearchProduct.class);
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}
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private static <R extends Result> void selectResultWithCountry(SparkSession spark, String inputPath, String outputPath, String country, String type, Class<R> inputClazz) {
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Utils.readPath(spark, inputPath + "/" + type, inputClazz)
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.filter((FilterFunction<R>) p -> !p.getDataInfo().getDeletedbyinference() && !p.getDataInfo().getInvisible() &&
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p.getCountry().stream().anyMatch(c -> c.getClassid().equals(country)))
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.map((MapFunction<R, String>) p -> p.getId(), Encoders.STRING() )
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.write()
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.option(COMPRESSION, GZIP)
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.mode(SaveMode.Append)
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.json(outputPath);
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}
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private static boolean isCountryInFunderJurisdiction(List<Field<String>> fundingtrees, String country) {
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try {
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final SAXReader reader = new SAXReader();
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reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
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for (Field<String> fundingtree: fundingtrees){
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final Document doc = reader.read(new StringReader(fundingtree.getValue()));
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if(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText().equals(country)){
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return true;
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}
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}
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return false;
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} catch (DocumentException | SAXException e) {
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throw new IllegalArgumentException(e);
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}
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}
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}
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