152 lines
5.0 KiB
Java
152 lines
5.0 KiB
Java
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import static eu.dnetlib.dhp.actionmanager.Constants.*;
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import static eu.dnetlib.dhp.actionmanager.Constants.UPDATE_CLASS_NAME;
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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.Arrays;
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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.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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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 com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize;
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import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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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 eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.schema.oaf.utils.PidType;
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import eu.dnetlib.dhp.utils.DHPUtils;
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public class PrepareBipFinder implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareBipFinder.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_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 sourcePath = parser.get("sourcePath");
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log.info("sourcePath {}: ", sourcePath);
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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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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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prepareResults(spark, sourcePath, outputPath);
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});
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}
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private static 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(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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.map((MapFunction<BipScore, Result>) v -> {
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Result r = new Result();
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final String cleanedPid = CleaningFunctions.normalizePidValue(PidType.doi.toString(), v.getId());
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r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), PidType.doi.toString()));
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Instance inst = new Instance();
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/*
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* inst .setPid( Arrays .asList( OafMapperUtils .structuredProperty( cleanedPid, OafMapperUtils
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* .qualifier( PidType.doi.toString(), DOI_CLASSNAME, ModelConstants.DNET_PID_TYPES,
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* ModelConstants.DNET_PID_TYPES), null)));
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*/
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r.setInstance(Arrays.asList(inst));
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/*
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* r .setDataInfo( OafMapperUtils .dataInfo( false, null, true, false, OafMapperUtils .qualifier(
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* ModelConstants.PROVENANCE_ENRICH, null, ModelConstants.DNET_PROVENANCE_ACTIONS,
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* ModelConstants.DNET_PROVENANCE_ACTIONS), null));
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*/
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return r;
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}, Encoders.bean(Result.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 + "/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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MeasureUnit u = new MeasureUnit();
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u.setValue(u.getValue());
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u.setKey(u.getKey());
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/*
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* kv .setDataInfo( OafMapperUtils .dataInfo( false, UPDATE_DATA_INFO_TYPE, true, false,
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* OafMapperUtils .qualifier( UPDATE_MEASURE_BIP_CLASS_ID, UPDATE_CLASS_NAME,
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* ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
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* ""));
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*/
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return u;
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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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