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

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

import java.io.Serializable;
import java.io.StringReader;
import java.util.List;
import java.util.Optional;

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.SparkSession;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.io.SAXReader;

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;

import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.skgif.model.MinGrant;
import eu.dnetlib.dhp.skgif.model.MinOrganization;
import eu.dnetlib.dhp.skgif.model.MinProduct;
import eu.dnetlib.dhp.skgif.model.Prefixes;
import eu.dnetlib.dhp.utils.DHPUtils;
import scala.Tuple2;

/**
 * @author miriam.baglioni
 * @Date 16/02/24
 */
public class Utils implements Serializable {
	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();

	private Utils() {
	}

	public static void removeOutputDir(SparkSession spark, String path) {
		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
	}

	public static <R> Dataset<R> readPath(
		SparkSession spark, String inputPath, Class<R> clazz) {
		return spark
			.read()
			.textFile(inputPath)
			.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
	}

	public static Tuple2<String, Boolean> getOrcid(List<StructuredProperty> pid) {
		if (!Optional.ofNullable(pid).isPresent())
			return null;
		if (pid.size() == 0)
			return null;
		for (StructuredProperty p : pid) {
			if (p.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
				return new Tuple2<>(p.getValue(), Boolean.TRUE);
			}
		}
		for (StructuredProperty p : pid) {
			if (p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING)) {
				return new Tuple2<>(p.getValue(), Boolean.FALSE);
			}
		}
		return null;
	}

	public static String getIdentifier(Prefixes entity, String id) {
		return entity.label + DHPUtils.md5(id);

	}

	public static String getFunderName(String fundingtree) throws DocumentException {
		final Document doc;

		doc = new SAXReader().read(new StringReader(fundingtree));
		// f.setShortName(((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText());
		return ((org.dom4j.Node) (doc.selectNodes("//funder/name").get(0))).getText();
		// f.setJurisdiction(((org.dom4j.Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText());

	}

	public static MinOrganization getMinOrganization(Organization o) {
		MinOrganization mo = new MinOrganization();
		// mo.setLocal_identifier(Utils.getIdentifier(Prefixes.ORGANIZATION, o.getId()));
		mo.setLocal_identifier(o.getId());
		if (Optional.ofNullable(o.getLegalname()).isPresent())
			mo.setName(o.getLegalname().getValue());
		if (Optional.ofNullable(o.getPid()).isPresent())
			for (StructuredProperty pid : o.getPid()) {
				if (Optional.ofNullable(pid.getQualifier()).isPresent() &&
					Optional.ofNullable(pid.getQualifier().getClassid()).isPresent())
					switch (pid.getQualifier().getClassid().toLowerCase()) {
						case "ror":
							mo.setRor(pid.getValue());
							break;
						case "isni":
							mo.setIsni(pid.getValue());
							break;
						case "fundref":
							mo.setFundRef(pid.getValue());
							break;
						case "ringgold":
							mo.setRinGold(pid.getValue());
							break;
						case "wikidata":
							mo.setWikidata(pid.getValue());
							break;

					}
			}
		return mo;
	}

	public static MinGrant getMinGrant(Project p) throws DocumentException {
		MinGrant mg = new MinGrant();
		// mg.setLocal_identifier(Utils.getIdentifier(Prefixes.GRANT, p.getId()));
		mg.setLocal_identifier(p.getId());
		if (Optional.ofNullable(p.getCode()).isPresent())
			mg.setCode(p.getCode().getValue());
		if (Optional.ofNullable(p.getFundingtree()).isPresent() && p.getFundingtree().size() > 0)
			mg.setFunder(getFunderName(p.getFundingtree().get(0).getValue()));
		if (Optional.ofNullable(p.getAcronym()).isPresent())
			mg.setTitle(p.getAcronym().getValue());
		else if (Optional.ofNullable(p.getTitle()).isPresent()) {
			mg.setTitle(p.getTitle().getValue());

		}
		return mg;
	}

	public static <R extends Result> MinProduct getMinProduct(R r) throws JsonProcessingException {
		MinProduct mp = new MinProduct();
		// mp.setLocal_identifier(Utils.getIdentifier(Prefixes.RESEARCH_PRODUCT, r.getId()));
		mp.setLocal_identifier(r.getId());
		for (StructuredProperty title : r.getTitle()) {
			if (title.getQualifier().getClassid().equalsIgnoreCase("main title")) {
				mp.setTitle(title.getValue());
			}
		}
		if (r.getPid() != null)
			for (StructuredProperty pid : r.getPid()) {
				switch (pid.getQualifier().getClassid().toLowerCase()) {
					case "doi":
						mp.setDoi(pid.getValue());
						break;
					case "pmcid":
						mp.setPmcid(pid.getValue());
						break;
					case "arxiv":
						mp.setArxivid(pid.getValue());
						break;
					case "pmid":
						mp.setPmid(pid.getValue());
						break;
				}
			}

		return mp;
	}
}