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