forked from D-Net/dnet-hadoop
165 lines
5.7 KiB
Java
165 lines
5.7 KiB
Java
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package eu.dnetlib.dhp.oa.graph.merge;
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import static eu.dnetlib.dhp.common.GraphSupport.deleteGraphTable;
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import static eu.dnetlib.dhp.common.GraphSupport.saveGraphTable;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.Objects;
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import java.util.Optional;
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import eu.dnetlib.dhp.common.GraphFormat;
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import eu.dnetlib.dhp.common.GraphSupport;
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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.FilterFunction;
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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 com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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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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/**
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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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* by eu.dnetlib.dhp.schema.common.ModelSupport#idFn()
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*/
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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 String PRIORITY_DEFAULT = "BETA"; // BETA | PROD
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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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CleanGraphSparkJob.class
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.getResourceAsStream(
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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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parser.parseArgument(args);
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String priority = Optional
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.ofNullable(parser.get("priority"))
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.orElse(PRIORITY_DEFAULT);
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log.info("priority: {}", priority);
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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 betaInputGraph = parser.get("betaInputGraph");
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log.info("betaInputGraph: {}", betaInputGraph);
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String prodInputGraph = parser.get("prodInputGraph");
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log.info("prodInputGraph: {}", prodInputGraph);
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String outputGraph = parser.get("outputGraph");
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log.info("outputGraph: {}", outputGraph);
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GraphFormat inputGraphFormat = Optional
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.ofNullable(parser.get("inputGraphFormat"))
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.map(GraphFormat::valueOf)
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.orElse(GraphFormat.DEFAULT);
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log.info("inputGraphFormat: {}", inputGraphFormat);
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GraphFormat outputGraphFormat = Optional
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.ofNullable(parser.get("outputGraphFormat"))
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.map(GraphFormat::valueOf)
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.orElse(GraphFormat.DEFAULT);
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log.info("outputGraphFormat: {}", outputGraphFormat);
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String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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Class<? extends Oaf> clazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
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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.registerKryoClasses(ModelSupport.getOafModelClasses());
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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deleteGraphTable(spark, clazz, outputGraph, outputGraphFormat);
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mergeGraphTable(spark, priority, betaInputGraph, prodInputGraph, clazz, clazz, outputGraph, inputGraphFormat, outputGraphFormat);
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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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SparkSession spark,
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String priority,
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String betaInputGraph,
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String prodInputGraph,
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Class<P> p_clazz,
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Class<B> b_clazz,
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String outputGraph, GraphFormat inputGraphFormat, GraphFormat outputGraphFormat) {
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Dataset<Tuple2<String, B>> beta = readGraph(spark, betaInputGraph, b_clazz, inputGraphFormat);
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Dataset<Tuple2<String, P>> prod = readGraph(spark, prodInputGraph, p_clazz, inputGraphFormat);
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Dataset<P> merged = prod
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.joinWith(beta, prod.col("_1").equalTo(beta.col("_1")), "full_outer")
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.map((MapFunction<Tuple2<Tuple2<String, P>, Tuple2<String, B>>, P>) value -> {
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Optional<P> p = Optional.ofNullable(value._1()).map(Tuple2::_2);
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Optional<B> b = Optional.ofNullable(value._2()).map(Tuple2::_2);
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switch (priority) {
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default:
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case "BETA":
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return mergeWithPriorityToBETA(p, b);
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case "PROD":
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return mergeWithPriorityToPROD(p, b);
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}
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}, Encoders.bean(p_clazz))
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.filter((FilterFunction<P>) Objects::nonNull);
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saveGraphTable(merged, p_clazz, outputGraph, outputGraphFormat);
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}
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private static <P extends Oaf, B extends Oaf> P mergeWithPriorityToPROD(Optional<P> p, Optional<B> b) {
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if (b.isPresent() & !p.isPresent()) {
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return (P) b.get();
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}
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if (p.isPresent()) {
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return p.get();
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}
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return null;
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}
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private static <P extends Oaf, B extends Oaf> P mergeWithPriorityToBETA(Optional<P> p, Optional<B> b) {
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if (p.isPresent() & !b.isPresent()) {
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return p.get();
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}
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if (b.isPresent()) {
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return (P) b.get();
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}
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return null;
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}
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private static <T extends Oaf> Dataset<Tuple2<String, T>> readGraph(
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SparkSession spark, String inputGraph, Class<T> clazz, GraphFormat inputGraphFormat) {
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log.info("Reading Graph table from: {}", inputGraph);
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return GraphSupport.readGraph(spark, inputGraph, clazz, inputGraphFormat)
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.map((MapFunction<T, Tuple2<String, T>>) 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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}, Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
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}
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}
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