132 lines
3.7 KiB
Java
132 lines
3.7 KiB
Java
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package eu.dnetlib.dhp.bypassactionset.bipfinder;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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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.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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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.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.bypassactionset.model.BipScore;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import scala.Tuple2;
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/**
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* created the Atomic Action for each tipe of results
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*/
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public class SparkUpdateBip implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkUpdateBip.class);
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public static <I extends Result> void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SparkUpdateBip.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/bypassactionset/bip_update_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("inputPath");
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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 bipScorePath = parser.get("bipScorePath");
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log.info("bipScorePath: {}", bipScorePath);
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
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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 -> updateBipFinder(spark, inputPath, outputPath, bipScorePath, inputClazz)
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);
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}
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private static <I extends Result> void updateBipFinder(SparkSession spark, String inputPath, String outputPath,
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String bipScorePath, Class<I> inputClazz) {
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Dataset<I> results = readPath(spark, inputPath, inputClazz);
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Dataset<BipScore> bipScores = readPath(spark, bipScorePath, BipScore.class);
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results
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.joinWith(bipScores, results.col("id").equalTo(bipScores.col("id")), "left")
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.map((MapFunction<Tuple2<I, BipScore>, I>) value -> {
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if (!Optional.ofNullable(value._2()).isPresent()) {
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return value._1();
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}
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value._1().setMeasures(getMeasure(value._2()));
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return value._1();
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}, Encoders.bean(inputClazz))
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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 + "/bip");
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}
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private static List<Measure> getMeasure(BipScore value) {
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return value
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.getScoreList()
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.stream()
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.map(score -> {
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Measure m = new Measure();
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m.setId(score.getId());
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m
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.setUnit(
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score
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.getUnit()
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.stream()
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.map(unit -> {
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KeyValue kv = new KeyValue();
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kv.setValue(unit.getValue());
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kv.setKey(unit.getKey());
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kv
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.setDataInfo(
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getDataInfo(
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UPDATE_DATA_INFO_TYPE,
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UPDATE_MEASURE_BIP_CLASS_ID,
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UPDATE_CLASS_NAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS, ""));
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return kv;
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})
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.collect(Collectors.toList()));
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return m;
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})
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.collect(Collectors.toList());
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}
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}
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