package eu.dnetlib.dhp.countrypropagation; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; import java.util.Arrays; import java.util.HashSet; import java.util.Set; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.*; import org.apache.spark.sql.Dataset; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; public class PrepareResultCountrySet { private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( PrepareResultCountrySet.class .getResourceAsStream( "/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = isSparkSessionManaged(parser); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String workingPath = parser.get("workingPath"); String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); final String datasourcecountrypath = parser.get("preparedInfoPath"); log.info("preparedInfoPath: {}", datasourcecountrypath); final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); Class resultClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); //conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); runWithSparkSession( conf, isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); getPotentialResultToUpdate( spark, inputPath, outputPath, datasourcecountrypath, workingPath, resultClazz); }); } private static void getPotentialResultToUpdate( SparkSession spark, String inputPath, String outputPath, String datasourcecountrypath, String workingPath, Class resultClazz) { // selects all the results non deleted by inference and non invisible Dataset result = readPath(spark, inputPath, resultClazz) .filter( (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && !r.getDataInfo().getInvisible()); // of the results collects the distinct keys for collected from (at the level of the result) and hosted by // and produces pairs resultId, key for each distinct key associated to the result result.flatMap((FlatMapFunction) r -> { Set cfhb = r.getCollectedfrom().stream().map(cf -> cf.getKey()).collect(Collectors.toSet()); cfhb.addAll(r.getInstance().stream().map(i -> i.getHostedby().getKey()).collect(Collectors.toSet())); return cfhb .stream() .map(value -> EntityEntityRel.newInstance(r.getId(), value)) .collect(Collectors.toList()) .iterator(); }, Encoders.bean(EntityEntityRel.class)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(workingPath + "/resultCfHb"); Dataset datasource_country = readPath(spark, datasourcecountrypath, DatasourceCountry.class); Dataset cfhb = readPath(spark, workingPath + "/resultCfHb", EntityEntityRel.class); datasource_country .joinWith( cfhb, cfhb .col("entity2Id") .equalTo(datasource_country.col("datasourceId"))) .groupByKey( (MapFunction, String>) t2 -> t2._2().getEntity1Id(), Encoders.STRING()) .mapGroups( (MapGroupsFunction, ResultCountrySet>) (k, it) -> { ResultCountrySet rcs = new ResultCountrySet(); rcs.setResultId(k); Set set = new HashSet<>(); Set countryCodes = new HashSet<>(); DatasourceCountry first = it.next()._1(); countryCodes.add(first.getCountry().getClassid()); set.add(first.getCountry()); it.forEachRemaining(t2 -> { if (!countryCodes.contains(t2._1().getCountry().getClassid())) set.add(t2._1().getCountry()); }); rcs.setCountrySet(new ArrayList<>(set)); return rcs; }, Encoders.bean(ResultCountrySet.class)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath); } }