dhp-graph-dump/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/skgif/DumpGrant.java

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

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

import java.io.Serializable;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;

import org.apache.avro.generic.GenericData;
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.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.*;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.EncloseMinElement;
import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.ExtendingOrganization;
import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.GrantRelation;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.skgif.model.*;
import scala.Tuple2;

/**
 * @author miriam.baglioni
 * @Date 22/02/24
 */
public class DumpGrant implements Serializable {
	private static final Logger log = LoggerFactory.getLogger(DumpGrant.class);

	public static void main(String[] args) throws Exception {
		String jsonConfiguration = IOUtils
			.toString(
				DumpGrant.class
					.getResourceAsStream(
						"/eu/dnetlib/dhp/oa/graph/dump/skgif/dump_grant_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 workingDir = parser.get("workingDir");
		log.info("workingDir: {}", workingDir);

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

		SparkConf conf = new SparkConf();

		runWithSparkSession(
			conf,
			isSparkSessionManaged,
			spark -> {
				Utils.removeOutputDir(spark, outputPath + "grants");

				mapGrants(spark, inputPath, outputPath, workingDir);
			});
	}

	private static void mapGrants(SparkSession spark, String inputPath, String outputPath, String workingDir) {
		Dataset<Project> projects = Utils
			.readPath(spark, inputPath + "project", Project.class)
			.filter(
				(FilterFunction<Project>) p -> !p.getDataInfo().getDeletedbyinference() &&
					!p.getDataInfo().getInvisible());
		Dataset<ExtendingOrganization> partecipatingOrgs = Utils
			.readPath(spark, workingDir + "relations/project_partecipating_organization", ExtendingOrganization.class);

		projects = projects
			.groupByKey((MapFunction<Project, String>) p -> p.getId(), Encoders.STRING())
			.mapGroups((MapGroupsFunction<String, Project, Project>) (k, v) -> v.next(), Encoders.bean(Project.class));
		projects
			.joinWith(partecipatingOrgs, projects.col("id").equalTo(partecipatingOrgs.col("entityId")), "left")
			.map((MapFunction<Tuple2<Project, ExtendingOrganization>, Grant>) t2 -> {
				Grant g = dumpGrant(t2._1());
				if (Optional.ofNullable(t2._2()).isPresent())
					g.setBeneficiaries(t2._2().getRelevant_organization());
				return g;
			}, Encoders.bean(Grant.class))
			.write()
			.mode(SaveMode.Overwrite)
			.option("compression", "gzip")
			.json(outputPath + "grants");
	}

	private static Grant dumpGrant(Project project) throws DocumentException {
		Grant g = new Grant();

		g.setLocal_identifier(project.getId());
		g.setGrantCode(project.getCode().getValue());
		g.setIdentifiers(getProjectIdentifier(project));
		if (Optional.ofNullable(project.getTitle()).isPresent())
			g.setTitle(project.getTitle().getValue());
		g
			.setSummary(
				Optional
					.ofNullable(project.getSummary())
					.map(value -> value.getValue())
					.orElse(new String()));
		g
			.setAcronym(
				Optional
					.ofNullable(project.getAcronym())
					.map(value -> value.getValue())
					.orElse(new String()));
		if (Optional.ofNullable(project.getFundingtree()).isPresent() &&
			project.getFundingtree().size() > 0) {
			g.setFunder(Utils.getFunderName(project.getFundingtree().get(0).getValue()));
			// * private String funding_stream;// fundingtree to be used the xpath //funding_level_[n]
			g.setFunding_stream(getFundingStream(project.getFundingtree().get(0).getValue()));
		}

		g
			.setCurrency(
				Optional
					.ofNullable(project.getCurrency())
					.map(value -> value.getValue())
					.orElse(new String()));
		g
			.setFunded_amount(
				Optional
					.ofNullable(project.getFundedamount())
					.orElse(null));
		if (Optional.ofNullable(project.getSubjects()).isPresent())
			g
				.setKeywords(
					project
						.getSubjects()
						.stream()
						.map(s -> s.getValue())
						.collect(Collectors.toList()));
		g
			.setStart_date(
				Optional
					.ofNullable(project.getStartdate())
					.map(value -> value.getValue())
					.orElse(new String()));
		g
			.setEnd_date(
				Optional
					.ofNullable(project.getEnddate())
					.map(value -> value.getValue())
					.orElse(new String()));
		g
			.setWebsite(
				Optional
					.ofNullable(project.getWebsiteurl())
					.map(value -> value.getValue())
					.orElse(new String()));
		return g;
	}

	private static String getFundingStream(String fundingtree) throws DocumentException {
		final Document doc;

		doc = new SAXReader().read(new StringReader(fundingtree));
		if (Optional.ofNullable(doc.selectNodes("//funding_level_0")).isPresent() &&
			doc.selectNodes("//funding_level_0").size() > 0 &&
			Optional.ofNullable(doc.selectNodes("//funding_level_0/name")).isPresent() &&
			doc.selectNodes("//funding_level_0/name").size() > 0)
			return ((org.dom4j.Node) (doc.selectNodes("//funding_level_0/name").get(0))).getText();
		return new String();

	}

	private static List<Identifier> getProjectIdentifier(Project project) throws DocumentException {
		List<Identifier> identifiers = new ArrayList<>();
		if (project.getPid().size() > 0)
			project
				.getPid()
				.stream()
				.forEach(p -> identifiers.add(Identifier.newInstance(p.getQualifier().getClassid(), p.getValue())));
		identifiers
			.add(
				Identifier
					.newInstance(
						Utils.getFunderName(project.getFundingtree().get(0).getValue()), project.getCode().getValue()));
		return identifiers;

	}
}