166 lines
6.2 KiB
Java
166 lines
6.2 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.funderresults;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.schema.dump.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import scala.Tuple2;
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/**
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* Preparation of the Project information to be added to the dumped results. For each result associated to at least one
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* Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the
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* list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to
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*/
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public class SparkPrepareResultProject implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SparkPrepareResultProject.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final String communityMapPath = parser.get("communityMapPath");
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log.info("communityMapPath: {}", communityMapPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Utils.removeOutputDir(spark, outputPath);
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prepareResultProjectList2(spark, inputPath, outputPath, communityMapPath);
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});
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}
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private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath,
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String communityMapPath) {
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CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
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Dataset<Relation> relation = Utils
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.readPath(spark, inputPath + "/relation", Relation.class)
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.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
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Dataset<eu.dnetlib.dhp.schema.oaf.Result> result = Utils
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.readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class)
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.union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class))
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.union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class))
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.union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class));
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result
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.joinWith(relation, result.col("id").equalTo(relation.col("target")))
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.groupByKey(
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(MapFunction<Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation>, String>) value -> value
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._2()
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.getSource()
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.substring(3, 15),
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Encoders.STRING())
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.mapGroups(
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(MapGroupsFunction<String, Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation>, Tuple2<String, FunderResults>>) (
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s, it) -> {
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Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation> first = it.next();
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FunderResults fr = new FunderResults();
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List<Result> resultList = new ArrayList<>();
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resultList.add(ResultMapper.map(first._1(), communityMap, true));
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it.forEachRemaining(c -> {
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resultList.add(ResultMapper.map(c._1(), communityMap, true));
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});
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fr.setResults(resultList);
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return new Tuple2<>(s, fr);
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}, Encoders.tuple(Encoders.STRING(), Encoders.bean(FunderResults.class)))
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.foreach(t -> {
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String funder = t._1();
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spark
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.createDataFrame(t._2.getResults(), Result.class)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/" + funder);
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});
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}
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private static void prepareResultProjectList2(SparkSession spark, String inputPath, String outputPath,
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String communityMapPath) {
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CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
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Dataset<Relation> relation = Utils
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.readPath(spark, inputPath + "/relation", Relation.class)
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.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
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Dataset<eu.dnetlib.dhp.schema.oaf.Result> result = Utils
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.readPath(spark, inputPath + "/publication", eu.dnetlib.dhp.schema.oaf.Result.class)
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.union(Utils.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Result.class))
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.union(Utils.readPath(spark, inputPath + "/otherresearchproduct", eu.dnetlib.dhp.schema.oaf.Result.class))
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.union(Utils.readPath(spark, inputPath + "/software", eu.dnetlib.dhp.schema.oaf.Result.class));
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result
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.joinWith(relation, result.col("id").equalTo(relation.col("target")))
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.groupByKey(
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(MapFunction<Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation>, String>) value -> value
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._2()
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.getSource()
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.substring(3, 15),
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Encoders.STRING())
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.mapGroups(
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(MapGroupsFunction<String, Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation>, String>) (s, it) -> {
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Tuple2<eu.dnetlib.dhp.schema.oaf.Result, Relation> first = it.next();
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List<Result> resultList = new ArrayList<>();
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resultList.add(ResultMapper.map(first._1(), communityMap, true));
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it.forEachRemaining(c -> {
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resultList.add(ResultMapper.map(c._1(), communityMap, true));
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});
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spark
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.createDataFrame(resultList, Result.class)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/" + s);
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return new String();
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}, Encoders.STRING());
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}
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}
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