dhp-graph-dump/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/country/SparkFindResultsRelatedToCountry.java

package eu.dnetlib.dhp.oa.graph.dump.country;

import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;

import java.io.Serializable;
import java.io.StringReader;
import java.util.*;

import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;

import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;

/**
 * @author miriam.baglioni
 * @Date 27/04/23
 * Finds the results id which are in relation with another entity having the given country
 * or that have that country in the country list
 */
public class SparkFindResultsRelatedToCountry implements Serializable {
	private static final Logger log = LoggerFactory.getLogger(SparkFindResultsRelatedToCountry.class);

	public static final String COMPRESSION = "compression";
	public static final String GZIP = "gzip";

	public static void main(String[] args) throws Exception {
		String jsonConfiguration = IOUtils
			.toString(
				SparkFindResultsRelatedToCountry.class
					.getResourceAsStream(
						"/eu/dnetlib/dhp/oa/graph/dump/result_related_country_parameters.json"));

		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
		parser.parseArgument(args);

		Boolean isSparkSessionManaged = Optional
			.ofNullable(parser.get("isSparkSessionManaged"))
			.map(Boolean::valueOf)
			.orElse(Boolean.TRUE);
		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);

		final String inputPath = parser.get("sourcePath");
		log.info("inputPath: {}", inputPath);

		final String outputPath = parser.get("outputPath");
		log.info("outputPath: {}", outputPath);

		final String country = parser.get("country");

		run(
			isSparkSessionManaged, inputPath, outputPath, country);

	}

	private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath,
		String country) {
		SparkConf conf = new SparkConf();

		runWithSparkSession(
			conf,
			isSparkSessionManaged,
			spark -> {
				findRelatedEntities(
					spark, inputPath, outputPath, country);
			});

	}

	public static <I extends eu.dnetlib.dhp.schema.oaf.Result> void findRelatedEntities(
		SparkSession spark,
		String inputPath,
		String outputPath,
		String country) {

		Dataset<Project> projectsInCountry = Utils
			.readPath(spark, inputPath + "/project", Project.class)
			.filter((FilterFunction<Project>) p -> isCountryInFunderJurisdiction(p.getFundingtree(), country));

		Dataset<Relation> relsProjectResults = Utils
			.readPath(spark, inputPath + "/relation", Relation.class)
			.filter(
				(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
					r.getRelClass().equals(ModelConstants.PRODUCES));

		projectsInCountry
			.joinWith(relsProjectResults, projectsInCountry.col("id").equalTo(relsProjectResults.col("source")))
			.map((MapFunction<Tuple2<Project, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
			.write()
			.option(COMPRESSION, GZIP)
			.mode(SaveMode.Overwrite)
			.text(outputPath);

		Dataset<Organization> organizationsInCountry = Utils
			.readPath(spark, inputPath + "/organization", Organization.class)
			.filter(
				(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference()
					&& o.getCountry().getClassid().equals(country));

		Dataset<Relation> relsOrganizationResults = Utils
			.readPath(spark, inputPath + "/relation", Relation.class)
			.filter(
				(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
					r.getRelClass().equals(ModelConstants.IS_AUTHOR_INSTITUTION_OF));

		organizationsInCountry
			.joinWith(
				relsOrganizationResults,
				organizationsInCountry.col("id").equalTo(relsOrganizationResults.col("source")))
			.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
			.write()
			.option(COMPRESSION, GZIP)
			.mode(SaveMode.Append)
			.text(outputPath);

		selectResultWithCountry(spark, inputPath, outputPath, country, "publication", Publication.class);
		selectResultWithCountry(
			spark, inputPath, outputPath, country, "dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
		selectResultWithCountry(spark, inputPath, outputPath, country, "software", Software.class);
		selectResultWithCountry(
			spark, inputPath, outputPath, country, "otherresearchproduct", OtherResearchProduct.class);

	}

	private static <R extends Result> void selectResultWithCountry(SparkSession spark, String inputPath,
		String outputPath, String country, String type, Class<R> inputClazz) {
		Utils
			.readPath(spark, inputPath + "/" + type, inputClazz)
			.filter(
				(FilterFunction<R>) p -> !p.getDataInfo().getDeletedbyinference() && !p.getDataInfo().getInvisible() &&
					p.getCountry() != null &&
					p.getCountry().stream().anyMatch(c -> c.getClassid().equals(country)))
			.map((MapFunction<R, String>) p -> p.getId(), Encoders.STRING())
			.write()
			.option(COMPRESSION, GZIP)
			.mode(SaveMode.Append)
			.text(outputPath);
	}

	private static boolean isCountryInFunderJurisdiction(List<Field<String>> fundingtrees, String country) {
		try {
			final SAXReader reader = new SAXReader();
			reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
			for (Field<String> fundingtree : fundingtrees) {
				final Document doc = reader.read(new StringReader(fundingtree.getValue()));
				if (((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText().equals(country)) {
					return true;
				}
			}
			return false;
		} catch (DocumentException | SAXException e) {
			throw new IllegalArgumentException(e);
		}
	}

}