package eu.dnetlib.dhp.bypassactionset; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.bypassactionset.model.BipScore; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; 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 scala.Tuple2; import java.io.Serializable; import java.util.List; import java.util.Optional; import java.util.stream.Collectors; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; /** * created the Atomic Action for each tipe of results */ public class SparkUpdateBip implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkUpdateBip.class); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( SparkUpdateBip.class .getResourceAsStream( "/eu/dnetlib/dhp/actionmanager/bipfinder/input_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("inputPath"); log.info("inputPath {}: ", inputPath); final String outputPath = parser.get("outputPath"); log.info("outputPath {}: ", outputPath); final String bipScorePath = parser.get("bipScorePath"); log.info("bipScorePath: {}", bipScorePath); final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); Class inputClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> updateBipFinder(spark, inputPath, outputPath, bipScorePath, inputClazz) ); } private static void updateBipFinder(SparkSession spark, String inputPath, String outputPath, String bipScorePath, Class inputClazz) { Dataset results = readPath(spark, inputPath, inputClazz); Dataset bipScores = readPath(spark, bipScorePath, BipScore.class); results.joinWith(bipScores, results.col("id").equalTo(bipScores.col("id")), "left") .map((MapFunction, I>) value -> { if (!Optional.ofNullable(value._2()).isPresent()){ return value._1(); } value._1().setMeasures(getMeasure(value._2())); return value._1(); }, Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression","gzip") .json(outputPath + "/bip"); } private static List getMeasure(BipScore value) { return value .getScoreList() .stream() .map(score -> { Measure m = new Measure(); m.setId(score.getId()); m .setUnit( score .getUnit() .stream() .map(unit -> { KeyValue kv = new KeyValue(); kv.setValue(unit.getValue()); kv.setKey(unit.getKey()); kv.setDataInfo(getDataInfo(UPDATE_DATA_INFO_TYPE, UPDATE_MEASURE_BIP_CLASS_ID, UPDATE_MEASURE_BIP_CLASS_NAME, ModelConstants.DNET_PROVENANCE_ACTIONS, "")); return kv; }) .collect(Collectors.toList())); return m; }) .collect(Collectors.toList()); } }