BrBETA_dnet-hadoop/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java

package eu.dnetlib.dhp.orcidtoresultfromsemrel;

import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;

import java.util.List;
import java.util.Optional;

import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
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.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.google.common.collect.Lists;

import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import scala.Tuple2;

public class SparkOrcidToResultFromSemRelJob {
	private static final Logger log = LoggerFactory.getLogger(SparkOrcidToResultFromSemRelJob.class);

	public static void main(String[] args) throws Exception {
		String jsonConfiguration = IOUtils
			.toString(
				SparkOrcidToResultFromSemRelJob.class
					.getResourceAsStream(
						"/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json"));

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

		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
		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 possibleUpdates = parser.get("possibleUpdatesPath");
		log.info("possibleUpdatesPath: {}", possibleUpdates);

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

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

		Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);

		SparkConf conf = new SparkConf();
		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));

		runWithSparkHiveSession(
			conf,
			isSparkSessionManaged,
			spark -> {
				removeOutputDir(spark, outputPath);
				if (saveGraph) {
					execPropagation(spark, possibleUpdates, inputPath, outputPath, resultClazz);
				}
			});
	}

	private static <R extends Result> void execPropagation(
		SparkSession spark,
		String possibleUpdatesPath,
		String inputPath,
		String outputPath,
		Class<R> resultClazz) {

		// read possible updates (resultId and list of possible orcid to add
		Dataset<ResultOrcidList> possible_updates = readPath(spark, possibleUpdatesPath, ResultOrcidList.class);
		// read the result we have been considering
		Dataset<R> result = readPath(spark, inputPath, resultClazz);
		// make join result left_outer with possible updates

		result
			.joinWith(
				possible_updates,
				result.col("id").equalTo(possible_updates.col("resultId")),
				"left_outer")
			.map(authorEnrichFn(), Encoders.bean(resultClazz))
			.write()
			.mode(SaveMode.Overwrite)
			.option("compression", "gzip")
			.json(outputPath);
	}

	private static <R extends Result> MapFunction<Tuple2<R, ResultOrcidList>, R> authorEnrichFn() {
		return value -> {
			R ret = value._1();
			Optional<ResultOrcidList> rol = Optional.ofNullable(value._2());
			if (rol.isPresent() && Optional.ofNullable(ret.getAuthor()).isPresent()) {
				List<Author> toenrich_author = ret.getAuthor();
				List<AutoritativeAuthor> autoritativeAuthors = rol.get().getAuthorList();
				for (Author author : toenrich_author) {
					if (!containsAllowedPid(author)) {
						enrichAuthor(author, autoritativeAuthors);
					}
				}
			}

			return ret;
		};
	}

	private static void enrichAuthor(Author a, List<AutoritativeAuthor> au) {
		PacePerson pp = new PacePerson(a.getFullname(), false);
		for (AutoritativeAuthor aa : au) {
			if (enrichAuthor(aa, a, pp.getNormalisedFirstName(), pp.getNormalisedSurname())) {
				return;
			}
		}
	}

	private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author,
		String author_name,
		String author_surname) {
		boolean toaddpid = false;

		if (StringUtils.isNotEmpty(autoritative_author.getSurname())) {
			if (StringUtils.isNotEmpty(author.getSurname())) {
				author_surname = author.getSurname();
			}
			if (StringUtils.isNotEmpty(author_surname)) {
				// have the same surname. Check the name
				if (autoritative_author
					.getSurname()
					.trim()
					.equalsIgnoreCase(author_surname.trim()) && StringUtils.isNotEmpty(autoritative_author.getName())) {
					if (StringUtils.isNotEmpty(author.getName())) {
						author_name = author.getName();
					}
					if (StringUtils.isNotEmpty(author_name)) {
						if (autoritative_author
							.getName()
							.trim()
							.equalsIgnoreCase(author_name.trim())) {
							toaddpid = true;
						}
						// they could be differently written (i.e. only the initials of the name
						// in one of the two
						else {
							if (autoritative_author
								.getName()
								.trim()
								.substring(0, 0)
								.equalsIgnoreCase(author_name.trim().substring(0, 0))) {
								toaddpid = true;
							}
						}
					}
				}
			}
		}
		if (toaddpid) {
			StructuredProperty p = new StructuredProperty();
			p.setValue(autoritative_author.getOrcid());
			p
				.setQualifier(
					getQualifier(
						ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES));
			p
				.setDataInfo(
					getDataInfo(
						PROPAGATION_DATA_INFO_TYPE,
						PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID,
						PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME,
						ModelConstants.DNET_PROVENANCE_ACTIONS));

			Optional<List<StructuredProperty>> authorPid = Optional.ofNullable(author.getPid());
			if (authorPid.isPresent()) {
				authorPid.get().add(p);
			} else {
				author.setPid(Lists.newArrayList(p));
			}

		}
		return toaddpid;
	}

	private static boolean containsAllowedPid(Author a) {
		Optional<List<StructuredProperty>> pids = Optional.ofNullable(a.getPid());
		if (!pids.isPresent()) {
			return false;
		}
		for (StructuredProperty pid : pids.get()) {
			if (ModelConstants.ORCID_PENDING.equalsIgnoreCase(pid.getQualifier().getClassid()) ||
				ModelConstants.ORCID.equalsIgnoreCase(pid.getQualifier().getClassid())) {
				return true;
			}
		}
		return false;
	}
}