[BypassAS] update of results for bipFinder and FOS
parent
a7d50c499b
commit
6f7ca539c6
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package eu.dnetlib.dhp.bypassactionset;
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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 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 scala.Tuple2;
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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 static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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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/actionmanager/bipfinder/input_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 ->
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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.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.setDataInfo(getDataInfo(UPDATE_DATA_INFO_TYPE,
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UPDATE_MEASURE_BIP_CLASS_ID,
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UPDATE_MEASURE_BIP_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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@ -0,0 +1,121 @@
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package eu.dnetlib.dhp.bypassactionset;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Measure;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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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 scala.Tuple2;
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import java.io.Serializable;
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import java.util.*;
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import java.util.stream.Collectors;
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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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public class SparkUpdateFOS implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkUpdateFOS.class);
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private final static String NULL = "NULL";
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private final static String DNET_RESULT_SUBJECT = "dnet:result_subject";
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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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SparkUpdateFOS.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/bipfinder/input_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 fosPath = parser.get("fosPath");
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log.info("fosPath: {}", fosPath);
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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 ->
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updateFos(spark, inputPath, outputPath, fosPath, inputClazz)
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);
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}
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private static <I extends Result> void updateFos(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<FOSDataModel> bipScores = readPath(spark, bipScorePath, FOSDataModel.class);
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results.joinWith(bipScores, results.col("id").equalTo(bipScores.col("id")), "left")
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.map((MapFunction<Tuple2<I,FOSDataModel>, 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().getSubject().addAll(getSubjects(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);
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}
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private static List<StructuredProperty> getSubjects(FOSDataModel fos) {
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return Arrays.asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3()))
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.stream()
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.filter(Objects::nonNull)
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.collect(Collectors.toList());
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}
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private static StructuredProperty getSubject(String sbj) {
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if (sbj.equals(NULL))
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return null;
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StructuredProperty sp = new StructuredProperty();
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sp.setValue(sbj);
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sp.setQualifier(getQualifier(FOS_CLASS_ID, FOS_CLASS_NAME, DNET_RESULT_SUBJECT));
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sp.setDataInfo(getDataInfo(UPDATE_DATA_INFO_TYPE,
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UPDATE_SUBJECT_FOS_CLASS_ID,
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UPDATE_SUBJECT_FOS_CLASS_NAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS, ""));
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return sp;
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}
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}
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@ -0,0 +1,15 @@
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package eu.dnetlib.dhp.bypassactionset;
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import org.jetbrains.annotations.NotNull;
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public class Utils {
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private static final String ID_PREFIX = "50|doi_________";
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@NotNull
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public static String getIdentifier(String d) {
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return ID_PREFIX +
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IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", d));
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}
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}
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@ -0,0 +1,89 @@
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package eu.dnetlib.dhp.bypassactionset.bipfinder;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.bypassactionset.SparkUpdateBip;
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import eu.dnetlib.dhp.bypassactionset.model.BipDeserialize;
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import eu.dnetlib.dhp.bypassactionset.model.BipScore;
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import eu.dnetlib.dhp.schema.oaf.Result;
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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.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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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 java.io.Serializable;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import static eu.dnetlib.dhp.bypassactionset.Utils.getIdentifier;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class PrepareBipFinder implements Serializable {
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private static final String DOI = "doi";
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private static final Logger log = LoggerFactory.getLogger(SparkUpdateBip.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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/actionmanager/bipfinder/input_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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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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prepareResults(spark, inputPath, outputPath);
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});
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}
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private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
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.textFile(inputPath)
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.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
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spark
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.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
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BipScore bs = new BipScore();
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bs.setId(getIdentifier(key));
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bs.setScoreList(entry.get(key));
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return bs;
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}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
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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);
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}
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}
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@ -1,4 +1,4 @@
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package eu.dnetlib.dhp.bypassactionset;
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package eu.dnetlib.dhp.bypassactionset.fos;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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@ -0,0 +1,30 @@
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package eu.dnetlib.dhp.bypassactionset.model;
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import java.io.Serializable;
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import java.util.List;
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/**
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* Rewriting of the bipFinder input data by extracting the identifier of the result (doi)
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*/
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public class BipScore implements Serializable {
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private String id; // doi
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private List<Score> scoreList; // unit as given in the inputfile
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public String getId() {
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return id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public List<Score> getScoreList() {
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return scoreList;
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}
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public void setScoreList(List<Score> scoreList) {
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this.scoreList = scoreList;
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}
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}
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