BrBETA_dnet-hadoop/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java

package eu.dnetlib.dhp.projecttoresult;

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

import java.util.Arrays;
import java.util.List;

import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;

import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation;
import eu.dnetlib.dhp.schema.oaf.Relation;

public class PrepareProjectResultsAssociation {
	private static final Logger log = LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();

	public static void main(String[] args) throws Exception {

		String jsonConfiguration = IOUtils
			.toString(
				PrepareProjectResultsAssociation.class
					.getResourceAsStream(
						"/eu/dnetlib/dhp/projecttoresult/input_prepareprojecttoresult_parameters.json"));

		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);

		parser.parseArgument(args);

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

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

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

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

		final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
		log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));

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

		runWithSparkHiveSession(
			conf,
			isSparkSessionManaged,
			spark -> {
				// removeOutputDir(spark, potentialUpdatePath);
				// removeOutputDir(spark, alreadyLinkedPath);
				prepareResultProjProjectResults(
					spark,
					inputPath,
					potentialUpdatePath,
					alreadyLinkedPath,
					allowedsemrel);
			});
	}

	private static void prepareResultProjProjectResults(
		SparkSession spark,
		String inputPath,
		String potentialUpdatePath,
		String alreadyLinkedPath,
		List<String> allowedsemrel) {
		JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
		Dataset<Relation> relation = spark
			.createDataset(
				sc
					.textFile(inputPath)
					.map(item -> OBJECT_MAPPER.readValue(item, Relation.class))
					.rdd(),
				Encoders.bean(Relation.class));

		relation.createOrReplaceTempView("relation");

		String query = "SELECT source, target "
			+ "       FROM relation "
			+ "       WHERE datainfo.deletedbyinference = false "
			+ "       AND relClass = '"
			+ RELATION_RESULT_PROJECT_REL_CLASS
			+ "'";

		Dataset<Row> resproj_relation = spark.sql(query);
		resproj_relation.createOrReplaceTempView("resproj_relation");

		query = "SELECT resultId, collect_set(projectId) projectSet "
			+ "FROM ( "
			+ "SELECT r1.target resultId, r2.target projectId "
			+ "      FROM (SELECT source, target "
			+ "            FROM relation "
			+ "            WHERE datainfo.deletedbyinference = false  "
			+ getConstraintList(" relClass = '", allowedsemrel)
			+ "            ) r1"
			+ "      JOIN resproj_relation r2 "
			+ "      ON r1.source = r2.source "
			+ "      ) tmp "
			+ "GROUP BY resultId ";
		// query =
		// "SELECT projectId, collect_set(resId) resultSet "
		// + "FROM ("
		// + " SELECT r1.target resId, r2.target projectId "
		// + " FROM (SELECT source, target "
		// + " FROM relation "
		// + " WHERE datainfo.deletedbyinference = false "
		// + getConstraintList(" relClass = '", allowedsemrel)
		// + ") r1"
		// + " JOIN resproj_relation r2 "
		// + " ON r1.source = r2.source "
		// + " ) tmp "
		// + "GROUP BY projectId ";

		spark
			.sql(query)
			.as(Encoders.bean(ResultProjectSet.class))
			// .toJSON()
			// .write()
			// .mode(SaveMode.Overwrite)
			// .option("compression", "gzip")
			// .text(potentialUpdatePath);
			.toJavaRDD()
			.map(r -> OBJECT_MAPPER.writeValueAsString(r))
			.saveAsTextFile(potentialUpdatePath, GzipCodec.class);

		query = "SELECT source resultId, collect_set(target) projectSet "
			+ "FROM resproj_relation "
			+ "GROUP BY source";

		spark
			.sql(query)
			.as(Encoders.bean(ResultProjectSet.class))
			// .toJSON()
			// .write()
			// .mode(SaveMode.Overwrite)
			// .option("compression", "gzip")
			// .text(alreadyLinkedPath);
			.toJavaRDD()
			.map(r -> OBJECT_MAPPER.writeValueAsString(r))
			.saveAsTextFile(alreadyLinkedPath, GzipCodec.class);
	}
}