dnet-hadoop/dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java

package eu.dnetlib.dhp.orcidtoresultfromsemrel;

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

import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
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.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class PrepareResultOrcidAssociationStep1 {
    private static final Logger log =
            LoggerFactory.getLogger(PrepareResultOrcidAssociationStep1.class);

    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();

    public static void main(String[] args) throws Exception {
        String jsonConfiguration =
                IOUtils.toString(
                        SparkOrcidToResultFromSemRelJob3.class.getResourceAsStream(
                                "/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_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 outputPath = parser.get("outputPath");
        log.info("outputPath: {}", outputPath);

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

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

        final String resultType =
                resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
        log.info("resultType: {}", resultType);

        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 -> {
                    if (isTest(parser)) {
                        removeOutputDir(spark, outputPath);
                    }
                    prepareInfo(
                            spark, inputPath, outputPath, resultClazz, resultType, allowedsemrel);
                });
    }

    private static <R extends Result> void prepareInfo(
            SparkSession spark,
            String inputPath,
            String outputPath,
            Class<R> resultClazz,
            String resultType,
            List<String> allowedsemrel) {

        // read the relation table and the table related to the result it is using
        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
        org.apache.spark.sql.Dataset<Relation> relation =
                spark.createDataset(
                        sc.textFile(inputPath + "/relation")
                                .map(item -> OBJECT_MAPPER.readValue(item, Relation.class))
                                .rdd(),
                        Encoders.bean(Relation.class));
        relation.createOrReplaceTempView("relation");

        log.info("Reading Graph table from: {}", inputPath + "/" + resultType);
        Dataset<R> result = readPathEntity(spark, inputPath + "/" + resultType, resultClazz);

        result.createOrReplaceTempView("result");

        getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath + "/" + resultType);
    }

    private static void getPossibleResultOrcidAssociation(
            SparkSession spark, List<String> allowedsemrel, String outputPath) {
        String query =
                " select target resultId, author authorList"
                        + " from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author "
                        + " from ( "
                        + " select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid "
                        + " from result "
                        + " lateral view explode (author) a as MyT "
                        + " lateral view explode (MyT.pid) p as MyP "
                        + " where MyP.qualifier.classid = 'ORCID') tmp "
                        + " group by id) r_t "
                        + " join ("
                        + " select source, target "
                        + " from relation "
                        + " where datainfo.deletedbyinference = false "
                        + getConstraintList(" relclass = '", allowedsemrel)
                        + ") rel_rel "
                        + " on source = id";

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