master #59
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@ -0,0 +1,81 @@
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package eu.dnetlib.dhp.common.action;
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import java.io.BufferedWriter;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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import java.nio.charset.StandardCharsets;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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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.common.DbClient;
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import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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public class ReadDatasourceMasterDuplicateFromDB {
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private static final Logger log = LoggerFactory.getLogger(ReadDatasourceMasterDuplicateFromDB.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String QUERY = "SELECT distinct dd.id as masterId, d.officialname as masterName, dd.duplicate as duplicateId "
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+
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"FROM dsm_dedup_services dd join dsm_services d on (dd.id = d.id);";
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public static int execute(String dbUrl, String dbUser, String dbPassword, String hdfsPath, String hdfsNameNode)
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throws IOException {
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int count = 0;
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try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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FSDataOutputStream fos = fileSystem.create(new Path(hdfsPath));
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log.info("running query: {}", QUERY);
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log.info("storing results in: {}", hdfsPath);
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try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) {
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dbClient.processResults(QUERY, rs -> writeMap(datasourceMasterMap(rs), writer));
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count++;
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}
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}
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return count;
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}
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private static MasterDuplicate datasourceMasterMap(ResultSet rs) {
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try {
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final MasterDuplicate md = new MasterDuplicate();
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final String duplicateId = rs.getString("duplicateId");
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final String masterId = rs.getString("masterId");
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final String masterName = rs.getString("masterName");
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md.setDuplicateId(OafMapperUtils.createOpenaireId(10, duplicateId, true));
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md.setMasterId(OafMapperUtils.createOpenaireId(10, masterId, true));
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md.setMasterName(masterName);
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return md;
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} catch (final SQLException e) {
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throw new RuntimeException(e);
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}
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}
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private static void writeMap(final MasterDuplicate dm, final BufferedWriter writer) {
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try {
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writer.write(OBJECT_MAPPER.writeValueAsString(dm));
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writer.newLine();
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} catch (final IOException e) {
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throw new RuntimeException(e);
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}
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}
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}
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@ -0,0 +1,38 @@
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package eu.dnetlib.dhp.common.action.model;
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import java.io.Serializable;
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/**
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* @author miriam.baglioni
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* @Date 21/07/22
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*/
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public class MasterDuplicate implements Serializable {
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private String duplicateId;
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private String masterId;
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private String masterName;
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public String getDuplicateId() {
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return duplicateId;
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}
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public void setDuplicateId(String duplicateId) {
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this.duplicateId = duplicateId;
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}
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public String getMasterId() {
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return masterId;
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}
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public void setMasterId(String masterId) {
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this.masterId = masterId;
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}
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public String getMasterName() {
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return masterName;
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}
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public void setMasterName(String masterName) {
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this.masterName = masterName;
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}
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}
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@ -0,0 +1,227 @@
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package eu.dnetlib.dhp.oa.graph.clean.cfhb;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.expressions.Aggregator;
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import org.jetbrains.annotations.NotNull;
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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.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
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import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
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import eu.dnetlib.dhp.schema.oaf.Instance;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import scala.Tuple2;
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public class CleanCfHbSparkJob {
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private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJob.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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CleanCountrySparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_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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String inputPath = parser.get("inputPath");
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log.info("inputPath: {}", inputPath);
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String resolvedPath = parser.get("resolvedPath");
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log.info("resolvedPath: {}", resolvedPath);
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String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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String dsMasterDuplicatePath = parser.get("masterDuplicatePath");
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log.info("masterDuplicatePath: {}", dsMasterDuplicatePath);
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String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
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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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HdfsSupport.remove(resolvedPath, spark.sparkContext().hadoopConfiguration());
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cleanCfHb(
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spark, inputPath, entityClazz, resolvedPath, dsMasterDuplicatePath, outputPath);
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});
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}
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private static <T extends Result> void cleanCfHb(SparkSession spark, String inputPath, Class<T> entityClazz,
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String resolvedPath, String masterDuplicatePath, String outputPath) {
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// read the master-duplicate tuples
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Dataset<MasterDuplicate> md = spark
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.read()
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.textFile(masterDuplicatePath)
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.map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class));
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// prepare the resolved CF|HB references with the corresponding EMPTY master ID
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Dataset<IdCfHbMapping> resolved = spark
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.read()
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.textFile(inputPath)
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.map(as(entityClazz), Encoders.bean(entityClazz))
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.flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class));
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// set the EMPTY master ID/NAME and save it
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resolved
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.joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId")))
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.map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class))
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.filter((FilterFunction<IdCfHbMapping>) m -> Objects.nonNull(m.getMasterId()))
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.write()
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.mode(SaveMode.Overwrite)
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.json(resolvedPath);
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// read again the resolved CF|HB mapping
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Dataset<IdCfHbMapping> resolvedDS = spark
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.read()
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.textFile(resolvedPath)
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.map(as(IdCfHbMapping.class), Encoders.bean(IdCfHbMapping.class));
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// read the result table
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Dataset<T> res = spark
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.read()
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.textFile(inputPath)
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.map(as(entityClazz), Encoders.bean(entityClazz));
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// Join the results with the resolved CF|HB mapping, apply the mapping and save it
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res
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.joinWith(resolvedDS, res.col("id").equalTo(resolvedDS.col("resultId")), "left")
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.groupByKey((MapFunction<Tuple2<T, IdCfHbMapping>, String>) t -> t._1().getId(), Encoders.STRING())
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.mapGroups(getMapGroupsFunction(), Encoders.bean(entityClazz))
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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 MapFunction<Tuple2<IdCfHbMapping, MasterDuplicate>, IdCfHbMapping> asIdCfHbMapping() {
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return t -> {
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final IdCfHbMapping mapping = t._1();
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Optional
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.ofNullable(t._2())
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.ifPresent(t2 -> {
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mapping.setMasterId(t2.getMasterId());
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mapping.setMasterName(t2.getMasterName());
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});
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return mapping;
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};
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}
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private static <T extends Result> FlatMapFunction<T, IdCfHbMapping> flattenCfHbFn() {
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return r -> Stream
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.concat(
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Optional
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.ofNullable(r.getCollectedfrom())
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.map(cf -> cf.stream().map(KeyValue::getKey))
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.orElse(Stream.empty()),
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Stream
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.concat(
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Optional
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.ofNullable(r.getInstance())
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.map(
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instances -> instances
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.stream()
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.map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse("")))
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.orElse(Stream.empty())
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.filter(StringUtils::isNotBlank),
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Optional
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.ofNullable(r.getInstance())
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.map(
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instances -> instances
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.stream()
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.map(
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i -> Optional
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.ofNullable(i.getCollectedfrom())
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.map(KeyValue::getKey)
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.orElse("")))
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.orElse(Stream.empty())
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.filter(StringUtils::isNotBlank)))
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.distinct()
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.filter(StringUtils::isNotBlank)
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.map(cfHb -> asIdCfHbMapping(r.getId(), cfHb))
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.iterator();
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}
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private static <T extends Result> MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T> getMapGroupsFunction() {
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return new MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T>() {
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@Override
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public T call(String key, Iterator<Tuple2<T, IdCfHbMapping>> values) {
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final Tuple2<T, IdCfHbMapping> first = values.next();
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final T res = first._1();
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updateResult(res, first._2());
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values.forEachRemaining(t -> updateResult(res, t._2()));
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return res;
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}
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private void updateResult(T res, IdCfHbMapping m) {
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if (Objects.nonNull(m)) {
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res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m));
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res.getInstance().forEach(i -> {
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updateKeyValue(i.getHostedby(), m);
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updateKeyValue(i.getCollectedfrom(), m);
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});
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}
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}
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private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) {
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if (kv.getKey().equals(a.getCfhb())) {
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kv.setKey(a.getMasterId());
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kv.setValue(a.getMasterName());
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}
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}
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};
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}
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private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) {
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IdCfHbMapping m = new IdCfHbMapping(resultId);
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m.setCfhb(cfHb);
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return m;
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}
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private static <R> MapFunction<String, R> as(Class<R> clazz) {
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return s -> OBJECT_MAPPER.readValue(s, clazz);
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}
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}
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|
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@ -0,0 +1,54 @@
|
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|
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package eu.dnetlib.dhp.oa.graph.clean.cfhb;
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|
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import java.io.Serializable;
|
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|
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public class IdCfHbMapping implements Serializable {
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private String resultId;
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private String cfhb;
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private String masterId;
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private String masterName;
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public IdCfHbMapping() {
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}
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public IdCfHbMapping(String id) {
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this.resultId = id;
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}
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public String getResultId() {
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return resultId;
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}
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|
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public void setResultId(String resultId) {
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this.resultId = resultId;
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}
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|
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public String getCfhb() {
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return cfhb;
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}
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|
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public void setCfhb(String cfhb) {
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this.cfhb = cfhb;
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}
|
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|
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public String getMasterId() {
|
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return masterId;
|
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}
|
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|
||||
public void setMasterId(String masterId) {
|
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this.masterId = masterId;
|
||||
}
|
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|
||||
public String getMasterName() {
|
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return masterName;
|
||||
}
|
||||
|
||||
public void setMasterName(String masterName) {
|
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this.masterName = masterName;
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue