package eu.dnetlib.dhp.bypassactionset; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Measure; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; 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.*; import java.util.stream.Collectors; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; public class SparkUpdateFOS implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkUpdateFOS.class); private final static String NULL = "NULL"; private final static String DNET_RESULT_SUBJECT = "dnet:result_subject"; public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( SparkUpdateFOS.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 fosPath = parser.get("fosPath"); log.info("fosPath: {}", fosPath); final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); Class inputClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> updateFos(spark, inputPath, outputPath, fosPath, inputClazz) ); } private static void updateFos(SparkSession spark, String inputPath, String outputPath, String bipScorePath, Class inputClazz) { Dataset results = readPath(spark, inputPath, inputClazz); Dataset bipScores = readPath(spark, bipScorePath, FOSDataModel.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().getSubject().addAll(getSubjects(value._2())); return value._1(); }, Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression","gzip") .json(outputPath); } private static List getSubjects(FOSDataModel fos) { return Arrays.asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3())) .stream() .filter(Objects::nonNull) .collect(Collectors.toList()); } private static StructuredProperty getSubject(String sbj) { if (sbj.equals(NULL)) return null; StructuredProperty sp = new StructuredProperty(); sp.setValue(sbj); sp.setQualifier(getQualifier(FOS_CLASS_ID, FOS_CLASS_NAME, DNET_RESULT_SUBJECT)); sp.setDataInfo(getDataInfo(UPDATE_DATA_INFO_TYPE, UPDATE_SUBJECT_FOS_CLASS_ID, UPDATE_SUBJECT_FOS_CLASS_NAME, ModelConstants.DNET_PROVENANCE_ACTIONS, "")); return sp; } }