forked from D-Net/dnet-hadoop
code formatting
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db8b90a156
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@ -1,11 +1,11 @@
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package eu.dnetlib.dhp.oa.graph.merge;
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package eu.dnetlib.dhp.oa.graph.merge;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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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 java.util.Objects;
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import eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob;
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import java.util.Optional;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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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.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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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.FilterFunction;
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@ -16,13 +16,16 @@ import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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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.Logger;
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import org.slf4j.LoggerFactory;
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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.oa.graph.clean.CleanGraphSparkJob;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import scala.Tuple2;
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import scala.Tuple2;
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import java.util.Objects;
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import java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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/**
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/**
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* Combines the content from two aggregator graph tables of the same type, entities (or relationships) with the same ids
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* Combines the content from two aggregator graph tables of the same type, entities (or relationships) with the same ids
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* are picked preferring those from the BETA aggregator rather then from PROD. The identity of a relationship is defined
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* are picked preferring those from the BETA aggregator rather then from PROD. The identity of a relationship is defined
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@ -30,101 +33,102 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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*/
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*/
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public class MergeGraphSparkJob {
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public class MergeGraphSparkJob {
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private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJob.class);
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private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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String jsonConfiguration = IOUtils
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.toString(
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.toString(
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CleanGraphSparkJob.class
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CleanGraphSparkJob.class
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.getResourceAsStream(
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/merge_graphs_parameters.json"));
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"/eu/dnetlib/dhp/oa/graph/merge_graphs_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String betaInputPath = parser.get("betaInputPath");
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String betaInputPath = parser.get("betaInputPath");
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log.info("betaInputPath: {}", betaInputPath);
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log.info("betaInputPath: {}", betaInputPath);
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String prodInputPath = parser.get("prodInputPath");
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String prodInputPath = parser.get("prodInputPath");
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log.info("prodInputPath: {}", prodInputPath);
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log.info("prodInputPath: {}", prodInputPath);
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String outputPath = parser.get("outputPath");
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String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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log.info("outputPath: {}", outputPath);
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String graphTableClassName = parser.get("graphTableClassName");
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String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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log.info("graphTableClassName: {}", graphTableClassName);
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Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
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Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
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SparkConf conf = new SparkConf();
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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runWithSparkSession(
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runWithSparkSession(
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conf,
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conf,
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isSparkSessionManaged,
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isSparkSessionManaged,
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spark -> {
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spark -> {
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removeOutputDir(spark, outputPath);
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removeOutputDir(spark, outputPath);
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mergeGraphTable(spark, betaInputPath, prodInputPath, entityClazz, entityClazz, outputPath);
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mergeGraphTable(spark, betaInputPath, prodInputPath, entityClazz, entityClazz, outputPath);
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});
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});
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}
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}
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private static <P extends Oaf, B extends Oaf> void mergeGraphTable(
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private static <P extends Oaf, B extends Oaf> void mergeGraphTable(
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SparkSession spark,
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SparkSession spark,
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String betaInputPath,
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String betaInputPath,
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String prodInputPath,
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String prodInputPath,
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Class<P> p_clazz,
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Class<P> p_clazz,
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Class<B> b_clazz,
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Class<B> b_clazz,
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String outputPath) {
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String outputPath) {
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Dataset<Tuple2<String, B>> beta = readTableFromPath(spark, betaInputPath, b_clazz);
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Dataset<Tuple2<String, B>> beta = readTableFromPath(spark, betaInputPath, b_clazz);
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Dataset<Tuple2<String, P>> prod = readTableFromPath(spark, prodInputPath, p_clazz);
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Dataset<Tuple2<String, P>> prod = readTableFromPath(spark, prodInputPath, p_clazz);
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prod.joinWith(beta, prod.col("_1").equalTo(beta.col("_1")), "full_outer")
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prod
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.map((MapFunction<Tuple2<Tuple2<String, P>, Tuple2<String, B>>, P>) value -> {
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.joinWith(beta, prod.col("_1").equalTo(beta.col("_1")), "full_outer")
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Optional<P> p = Optional.ofNullable(value._1()).map(Tuple2::_2);
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.map((MapFunction<Tuple2<Tuple2<String, P>, Tuple2<String, B>>, P>) value -> {
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Optional<B> b = Optional.ofNullable(value._2()).map(Tuple2::_2);
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Optional<P> p = Optional.ofNullable(value._1()).map(Tuple2::_2);
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if (p.isPresent() & !b.isPresent()) {
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Optional<B> b = Optional.ofNullable(value._2()).map(Tuple2::_2);
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return p.get();
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if (p.isPresent() & !b.isPresent()) {
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}
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return p.get();
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if (b.isPresent()) {
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}
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return (P) b.get();
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if (b.isPresent()) {
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}
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return (P) b.get();
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return null;
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}
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}, Encoders.bean(p_clazz))
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return null;
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.filter((FilterFunction<P>) Objects::nonNull)
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}, Encoders.bean(p_clazz))
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.write()
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.filter((FilterFunction<P>) Objects::nonNull)
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.mode(SaveMode.Overwrite)
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.json(outputPath);
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.option("compression", "gzip")
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}
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.json(outputPath);
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}
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private static <T extends Oaf> Dataset<Tuple2<String, T>> readTableFromPath(
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private static <T extends Oaf> Dataset<Tuple2<String, T>> readTableFromPath(
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SparkSession spark, String inputEntityPath, Class<T> clazz) {
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SparkSession spark, String inputEntityPath, Class<T> clazz) {
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log.info("Reading Graph table from: {}", inputEntityPath);
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log.info("Reading Graph table from: {}", inputEntityPath);
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return spark
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return spark
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.read()
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.read()
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.textFile(inputEntityPath)
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.textFile(inputEntityPath)
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.map(
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.map(
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(MapFunction<String, Tuple2<String, T>>) value -> {
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(MapFunction<String, Tuple2<String, T>>) value -> {
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final T t = OBJECT_MAPPER.readValue(value, clazz);
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final T t = OBJECT_MAPPER.readValue(value, clazz);
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final String id = ModelSupport.idFn().apply(t);
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final String id = ModelSupport.idFn().apply(t);
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return new Tuple2<>(id, t);
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return new Tuple2<>(id, t);
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},
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},
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
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}
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}
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private static void removeOutputDir(SparkSession spark, String path) {
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private static void removeOutputDir(SparkSession spark, String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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}
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}
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}
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