forked from D-Net/dnet-hadoop
WIP: added oozie workflow for grouping graph entities by id
This commit is contained in:
parent
75324ae58a
commit
13e36a4da0
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@ -0,0 +1,2 @@
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package eu.dnetlib.dhp.schema.oaf;public class OafMapperUtils {
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}
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@ -0,0 +1,2 @@
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package eu.dnetlib.dhp.schema.oaf;public class ResultTypeComparator {
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}
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@ -0,0 +1,87 @@
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package eu.dnetlib.dhp.oa.graph.fuse;
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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.raw.MigrateMongoMdstoresApplication;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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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.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 java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class DispatchEntitiesSparkJob {
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private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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MigrateMongoMdstoresApplication.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dispatch_entities_bytype_parameters.json")));
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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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final String targetPath = parser.get("graphRawPath");
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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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removeOutputDir(spark, targetPath);
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ModelSupport.oafTypes
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.values()
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.forEach(clazz -> processEntity(spark, clazz, sourcePath, targetPath));
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});
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}
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private static <T extends Oaf> void processEntity(
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final SparkSession spark,
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final Class<T> clazz,
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final String sourcePath,
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final String targetPath) {
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final String type = clazz.getSimpleName().toLowerCase();
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log.info("Processing entities ({}) in file: {}", type, sourcePath);
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spark
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.read()
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.textFile(sourcePath)
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.filter((FilterFunction<String>) value -> isEntityType(value, type))
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.map(
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(MapFunction<String, String>) l -> StringUtils.substringAfter(l, "|"),
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Encoders.STRING())
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.text(targetPath + "/" + type);
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}
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private static boolean isEntityType(final String line, final String type) {
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return StringUtils.substringBefore(line, "|").equalsIgnoreCase(type);
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}
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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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}
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}
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@ -0,0 +1,186 @@
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package eu.dnetlib.dhp.oa.graph.groupbyid;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
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import java.io.IOException;
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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 org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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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.*;
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import org.apache.spark.sql.expressions.Aggregator;
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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 com.jayway.jsonpath.JsonPath;
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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.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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* Groups the graph content by entity identifier to ensure ID uniqueness
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*/
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public class GroupEntitiesSparkJob {
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private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class);
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private final static String ID_JPATH = "$.id";
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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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GroupEntitiesSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/group_graph_entities_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 graphInputPath = parser.get("graphInputPath");
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log.info("graphInputPath: {}", graphInputPath);
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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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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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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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groupEntities(spark, graphInputPath, outputPath);
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});
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}
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private static void groupEntities(
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SparkSession spark,
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String inputPath,
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String outputPath) {
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TypedColumn<Oaf, Oaf> aggregator = new GroupingAggregator().toColumn();
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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spark
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.read()
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.textFile(toSeq(listEntityPaths(inputPath, sc)))
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.map((MapFunction<String, Oaf>) s -> parseEntity(s), Encoders.kryo(Oaf.class))
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.groupByKey((MapFunction<Oaf, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
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.agg(aggregator)
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.map((MapFunction<Tuple2<String, Oaf>, Oaf>) Tuple2::_2, Encoders.kryo(Oaf.class))
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.write()
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.mode(SaveMode.Overwrite)
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.save(outputPath);
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}
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public static class GroupingAggregator extends Aggregator<Oaf, Oaf, Oaf> {
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@Override
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public Oaf zero() {
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return null;
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}
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@Override
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public Oaf reduce(Oaf b, Oaf a) {
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return mergeAndGet(b, a);
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}
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private Oaf mergeAndGet(Oaf b, Oaf a) {
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if (Objects.nonNull(a) && Objects.nonNull(b)) {
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return OafMapperUtils.merge(b, a);
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}
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return Objects.isNull(a) ? b : a;
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}
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@Override
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public Oaf merge(Oaf b, Oaf a) {
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return mergeAndGet(b, a);
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}
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@Override
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public Oaf finish(Oaf j) {
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return j;
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}
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@Override
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public Encoder<Oaf> bufferEncoder() {
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return Encoders.kryo(Oaf.class);
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}
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@Override
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public Encoder<Oaf> outputEncoder() {
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return Encoders.kryo(Oaf.class);
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}
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}
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private static <T extends Oaf> Oaf parseEntity(String s) {
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String prefix = StringUtils.substringBefore(jPath(ID_JPATH, s), "|");
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try {
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switch (prefix) {
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case "10":
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return OBJECT_MAPPER.readValue(s, Datasource.class);
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case "20":
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return OBJECT_MAPPER.readValue(s, Organization.class);
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case "40":
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return OBJECT_MAPPER.readValue(s, Project.class);
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case "50":
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String resultType = jPath("$.resulttype.classid", s);
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switch (resultType) {
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case "publication":
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return OBJECT_MAPPER.readValue(s, Publication.class);
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case "dataset":
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return OBJECT_MAPPER.readValue(s, eu.dnetlib.dhp.schema.oaf.Dataset.class);
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case "software":
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return OBJECT_MAPPER.readValue(s, Software.class);
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case "other":
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return OBJECT_MAPPER.readValue(s, OtherResearchProduct.class);
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default:
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throw new IllegalArgumentException(String.format("invalid resultType: '%s'", resultType));
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}
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default:
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throw new IllegalArgumentException(String.format("invalid id prefix: '%s'", prefix));
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}
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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private static List<String> listEntityPaths(String inputPath, JavaSparkContext sc) {
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return HdfsSupport
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.listFiles(inputPath, sc.hadoopConfiguration())
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.stream()
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.filter(p -> !p.contains("relation"))
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.collect(Collectors.toList());
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}
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private static String jPath(final String path, final String json) {
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Object o = JsonPath.read(json, path);
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if (o instanceof String)
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return (String) o;
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throw new IllegalStateException(String.format("could not extract '%s' from:\n%s", path, json));
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}
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}
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@ -33,9 +33,9 @@ import scala.Tuple2;
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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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public class MergeGraphTableSparkJob {
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private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJob.class);
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private static final Logger log = LoggerFactory.getLogger(MergeGraphTableSparkJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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@ -4,11 +4,9 @@ package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.util.Arrays;
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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.*;
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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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@ -20,6 +18,7 @@ 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.SparkSession;
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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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@ -29,16 +28,7 @@ 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.raw.common.VocabularyGroup;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
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import eu.dnetlib.dhp.schema.oaf.Project;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Software;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import scala.Tuple2;
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@ -113,7 +103,7 @@ public class GenerateEntitiesApplication {
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inputRdd
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.mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
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.reduceByKey((o1, o2) -> merge(o1, o2))
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.reduceByKey((o1, o2) -> OafMapperUtils.merge(o1, o2))
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.map(Tuple2::_2)
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.map(
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oaf -> oaf.getClass().getSimpleName().toLowerCase()
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@ -122,17 +112,6 @@ public class GenerateEntitiesApplication {
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.saveAsTextFile(targetPath, GzipCodec.class);
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}
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private static Oaf merge(final Oaf o1, final Oaf o2) {
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if (ModelSupport.isSubClass(o1, OafEntity.class)) {
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((OafEntity) o1).mergeFrom((OafEntity) o2);
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} else if (ModelSupport.isSubClass(o1, Relation.class)) {
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((Relation) o1).mergeFrom((Relation) o2);
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} else {
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throw new RuntimeException("invalid Oaf type:" + o1.getClass().getCanonicalName());
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}
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return o1;
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}
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private static List<Oaf> convertToListOaf(
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final String id,
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final String s,
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|
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@ -1,273 +0,0 @@
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package eu.dnetlib.dhp.oa.graph.raw.common;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Map;
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import java.util.Objects;
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import java.util.concurrent.ConcurrentHashMap;
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import java.util.function.Function;
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import java.util.function.Predicate;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.ExtraInfo;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.Journal;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.OAIProvenance;
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import eu.dnetlib.dhp.schema.oaf.OriginDescription;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.utils.DHPUtils;
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public class OafMapperUtils {
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public static KeyValue keyValue(final String k, final String v) {
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final KeyValue kv = new KeyValue();
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kv.setKey(k);
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kv.setValue(v);
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return kv;
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}
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public static List<KeyValue> listKeyValues(final String... s) {
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if (s.length % 2 > 0) {
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throw new RuntimeException("Invalid number of parameters (k,v,k,v,....)");
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}
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final List<KeyValue> list = new ArrayList<>();
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for (int i = 0; i < s.length; i += 2) {
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list.add(keyValue(s[i], s[i + 1]));
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}
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return list;
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}
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public static <T> Field<T> field(final T value, final DataInfo info) {
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if (value == null || StringUtils.isBlank(value.toString())) {
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return null;
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}
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final Field<T> field = new Field<>();
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field.setValue(value);
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field.setDataInfo(info);
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return field;
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}
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public static List<Field<String>> listFields(final DataInfo info, final String... values) {
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return Arrays
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.stream(values)
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.map(v -> field(v, info))
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.filter(Objects::nonNull)
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.filter(distinctByKey(f -> f.getValue()))
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.collect(Collectors.toList());
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}
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public static List<Field<String>> listFields(final DataInfo info, final List<String> values) {
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return values
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.stream()
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.map(v -> field(v, info))
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.filter(Objects::nonNull)
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.filter(distinctByKey(f -> f.getValue()))
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.collect(Collectors.toList());
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}
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public static Qualifier unknown(final String schemeid, final String schemename) {
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return qualifier("UNKNOWN", "Unknown", schemeid, schemename);
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}
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public static Qualifier qualifier(
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final String classid,
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final String classname,
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final String schemeid,
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final String schemename) {
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final Qualifier q = new Qualifier();
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q.setClassid(classid);
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q.setClassname(classname);
|
||||
q.setSchemeid(schemeid);
|
||||
q.setSchemename(schemename);
|
||||
return q;
|
||||
}
|
||||
|
||||
public static StructuredProperty structuredProperty(
|
||||
final String value,
|
||||
final String classid,
|
||||
final String classname,
|
||||
final String schemeid,
|
||||
final String schemename,
|
||||
final DataInfo dataInfo) {
|
||||
|
||||
return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
|
||||
}
|
||||
|
||||
public static StructuredProperty structuredProperty(
|
||||
final String value,
|
||||
final Qualifier qualifier,
|
||||
final DataInfo dataInfo) {
|
||||
if (value == null) {
|
||||
return null;
|
||||
}
|
||||
final StructuredProperty sp = new StructuredProperty();
|
||||
sp.setValue(value);
|
||||
sp.setQualifier(qualifier);
|
||||
sp.setDataInfo(dataInfo);
|
||||
return sp;
|
||||
}
|
||||
|
||||
public static ExtraInfo extraInfo(
|
||||
final String name,
|
||||
final String value,
|
||||
final String typology,
|
||||
final String provenance,
|
||||
final String trust) {
|
||||
final ExtraInfo info = new ExtraInfo();
|
||||
info.setName(name);
|
||||
info.setValue(value);
|
||||
info.setTypology(typology);
|
||||
info.setProvenance(provenance);
|
||||
info.setTrust(trust);
|
||||
return info;
|
||||
}
|
||||
|
||||
public static OAIProvenance oaiIProvenance(
|
||||
final String identifier,
|
||||
final String baseURL,
|
||||
final String metadataNamespace,
|
||||
final Boolean altered,
|
||||
final String datestamp,
|
||||
final String harvestDate) {
|
||||
|
||||
final OriginDescription desc = new OriginDescription();
|
||||
desc.setIdentifier(identifier);
|
||||
desc.setBaseURL(baseURL);
|
||||
desc.setMetadataNamespace(metadataNamespace);
|
||||
desc.setAltered(altered);
|
||||
desc.setDatestamp(datestamp);
|
||||
desc.setHarvestDate(harvestDate);
|
||||
|
||||
final OAIProvenance p = new OAIProvenance();
|
||||
p.setOriginDescription(desc);
|
||||
|
||||
return p;
|
||||
}
|
||||
|
||||
public static Journal journal(
|
||||
final String name,
|
||||
final String issnPrinted,
|
||||
final String issnOnline,
|
||||
final String issnLinking,
|
||||
final DataInfo dataInfo) {
|
||||
return journal(
|
||||
name,
|
||||
issnPrinted,
|
||||
issnOnline,
|
||||
issnLinking,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
dataInfo);
|
||||
}
|
||||
|
||||
public static Journal journal(
|
||||
final String name,
|
||||
final String issnPrinted,
|
||||
final String issnOnline,
|
||||
final String issnLinking,
|
||||
final String ep,
|
||||
final String iss,
|
||||
final String sp,
|
||||
final String vol,
|
||||
final String edition,
|
||||
final String conferenceplace,
|
||||
final String conferencedate,
|
||||
final DataInfo dataInfo) {
|
||||
|
||||
if (StringUtils.isNotBlank(name)
|
||||
|| StringUtils.isNotBlank(issnPrinted)
|
||||
|| StringUtils.isNotBlank(issnOnline)
|
||||
|| StringUtils.isNotBlank(issnLinking)) {
|
||||
final Journal j = new Journal();
|
||||
j.setName(name);
|
||||
j.setIssnPrinted(issnPrinted);
|
||||
j.setIssnOnline(issnOnline);
|
||||
j.setIssnLinking(issnLinking);
|
||||
j.setEp(ep);
|
||||
j.setIss(iss);
|
||||
j.setSp(sp);
|
||||
j.setVol(vol);
|
||||
j.setEdition(edition);
|
||||
j.setConferenceplace(conferenceplace);
|
||||
j.setConferencedate(conferencedate);
|
||||
j.setDataInfo(dataInfo);
|
||||
return j;
|
||||
} else {
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
public static DataInfo dataInfo(
|
||||
final Boolean deletedbyinference,
|
||||
final String inferenceprovenance,
|
||||
final Boolean inferred,
|
||||
final Boolean invisible,
|
||||
final Qualifier provenanceaction,
|
||||
final String trust) {
|
||||
final DataInfo d = new DataInfo();
|
||||
d.setDeletedbyinference(deletedbyinference);
|
||||
d.setInferenceprovenance(inferenceprovenance);
|
||||
d.setInferred(inferred);
|
||||
d.setInvisible(invisible);
|
||||
d.setProvenanceaction(provenanceaction);
|
||||
d.setTrust(trust);
|
||||
return d;
|
||||
}
|
||||
|
||||
public static String createOpenaireId(
|
||||
final int prefix,
|
||||
final String originalId,
|
||||
final boolean to_md5) {
|
||||
if (StringUtils.isBlank(originalId)) {
|
||||
return null;
|
||||
} else if (to_md5) {
|
||||
final String nsPrefix = StringUtils.substringBefore(originalId, "::");
|
||||
final String rest = StringUtils.substringAfter(originalId, "::");
|
||||
return String.format("%s|%s::%s", prefix, nsPrefix, DHPUtils.md5(rest));
|
||||
} else {
|
||||
return String.format("%s|%s", prefix, originalId);
|
||||
}
|
||||
}
|
||||
|
||||
public static String createOpenaireId(
|
||||
final String type,
|
||||
final String originalId,
|
||||
final boolean to_md5) {
|
||||
switch (type) {
|
||||
case "datasource":
|
||||
return createOpenaireId(10, originalId, to_md5);
|
||||
case "organization":
|
||||
return createOpenaireId(20, originalId, to_md5);
|
||||
case "person":
|
||||
return createOpenaireId(30, originalId, to_md5);
|
||||
case "project":
|
||||
return createOpenaireId(40, originalId, to_md5);
|
||||
default:
|
||||
return createOpenaireId(50, originalId, to_md5);
|
||||
}
|
||||
}
|
||||
|
||||
public static String asString(final Object o) {
|
||||
return o == null ? "" : o.toString();
|
||||
}
|
||||
|
||||
public static <T> Predicate<T> distinctByKey(
|
||||
final Function<? super T, ?> keyExtractor) {
|
||||
final Map<Object, Boolean> seen = new ConcurrentHashMap<>();
|
||||
return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,20 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "s",
|
||||
"paramLongName": "sourcePath",
|
||||
"paramDescription": "the source path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "g",
|
||||
"paramLongName": "graphRawPath",
|
||||
"paramDescription": "the path of the graph Raw in hdfs",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,20 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "gin",
|
||||
"paramLongName": "graphInputPath",
|
||||
"paramDescription": "the graph root path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "out",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the output merged graph root path",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,271 @@
|
|||
<workflow-app name="fuse graph entities by id" xmlns="uri:oozie:workflow:0.5">
|
||||
|
||||
<parameters>
|
||||
<property>
|
||||
<name>graphInputPath</name>
|
||||
<description>the graph root input path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the graph root output path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozieActionShareLibForSpark2</name>
|
||||
<description>oozie action sharelib for spark 2.*</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||
<description>spark 2.* extra listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||
<description>spark 2.* sql query execution listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<description>spark 2.* yarn history server address</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<description>spark 2.* event log dir location</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="fuse_graph"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="fuse_graph">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Fuse graph entities by ID</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.fuse.FuseGraphResultsSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--graphInputPath</arg><arg>${graphInputPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/entities</arg>
|
||||
</spark>
|
||||
<ok to="wait_merge"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="merge_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge datasets</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--betaInputPath</arg><arg>${betaInputGgraphPath}/dataset</arg>
|
||||
<arg>--prodInputPath</arg><arg>${prodInputGgraphPath}/dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/dataset</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--priority</arg><arg>${priority}</arg>
|
||||
</spark>
|
||||
<ok to="wait_merge"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="merge_otherresearchproduct">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge otherresearchproducts</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--betaInputPath</arg><arg>${betaInputGgraphPath}/otherresearchproduct</arg>
|
||||
<arg>--prodInputPath</arg><arg>${prodInputGgraphPath}/otherresearchproduct</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--priority</arg><arg>${priority}</arg>
|
||||
</spark>
|
||||
<ok to="wait_merge"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="merge_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge softwares</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--betaInputPath</arg><arg>${betaInputGgraphPath}/software</arg>
|
||||
<arg>--prodInputPath</arg><arg>${prodInputGgraphPath}/software</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--priority</arg><arg>${priority}</arg>
|
||||
</spark>
|
||||
<ok to="wait_merge"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="merge_datasource">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge datasources</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--betaInputPath</arg><arg>${betaInputGgraphPath}/datasource</arg>
|
||||
<arg>--prodInputPath</arg><arg>${prodInputGgraphPath}/datasource</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
|
||||
<arg>--priority</arg><arg>${priority}</arg>
|
||||
</spark>
|
||||
<ok to="wait_merge"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="merge_organization">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge organizations</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--betaInputPath</arg><arg>${betaInputGgraphPath}/organization</arg>
|
||||
<arg>--prodInputPath</arg><arg>${prodInputGgraphPath}/organization</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/organization</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
|
||||
<arg>--priority</arg><arg>${priority}</arg>
|
||||
</spark>
|
||||
<ok to="wait_merge"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="merge_project">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge projects</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--betaInputPath</arg><arg>${betaInputGgraphPath}/project</arg>
|
||||
<arg>--prodInputPath</arg><arg>${prodInputGgraphPath}/project</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
|
||||
<arg>--priority</arg><arg>${priority}</arg>
|
||||
</spark>
|
||||
<ok to="wait_merge"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="merge_relation">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--betaInputPath</arg><arg>${betaInputGgraphPath}/relation</arg>
|
||||
<arg>--prodInputPath</arg><arg>${prodInputGgraphPath}/relation</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
|
||||
<arg>--priority</arg><arg>${priority}</arg>
|
||||
</spark>
|
||||
<ok to="wait_merge"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait_merge" to="End"/>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -76,7 +76,7 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge publications</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphSparkJob</class>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -103,7 +103,7 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge datasets</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphSparkJob</class>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -130,7 +130,7 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge otherresearchproducts</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphSparkJob</class>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -157,7 +157,7 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge softwares</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphSparkJob</class>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -184,7 +184,7 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge datasources</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphSparkJob</class>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -211,7 +211,7 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge organizations</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphSparkJob</class>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -238,7 +238,7 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge projects</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphSparkJob</class>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -265,7 +265,7 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphSparkJob</class>
|
||||
<class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
|
|||
|
||||
import eu.dnetlib.dhp.schema.oaf.Datasource;
|
||||
|
||||
public class MergeGraphSparkJobTest {
|
||||
public class MergeGraphTableSparkJobTest {
|
||||
|
||||
private ObjectMapper mapper;
|
||||
|
||||
|
|
@ -28,7 +28,7 @@ public class MergeGraphSparkJobTest {
|
|||
public void testMergeDatasources() throws IOException {
|
||||
assertEquals(
|
||||
"openaire-cris_1.1",
|
||||
MergeGraphSparkJob
|
||||
MergeGraphTableSparkJob
|
||||
.mergeDatasource(
|
||||
d("datasource_cris.json"),
|
||||
d("datasource_UNKNOWN.json"))
|
||||
|
|
@ -36,7 +36,7 @@ public class MergeGraphSparkJobTest {
|
|||
.getClassid());
|
||||
assertEquals(
|
||||
"openaire-cris_1.1",
|
||||
MergeGraphSparkJob
|
||||
MergeGraphTableSparkJob
|
||||
.mergeDatasource(
|
||||
d("datasource_UNKNOWN.json"),
|
||||
d("datasource_cris.json"))
|
||||
|
|
@ -44,7 +44,7 @@ public class MergeGraphSparkJobTest {
|
|||
.getClassid());
|
||||
assertEquals(
|
||||
"driver-openaire2.0",
|
||||
MergeGraphSparkJob
|
||||
MergeGraphTableSparkJob
|
||||
.mergeDatasource(
|
||||
d("datasource_native.json"),
|
||||
d("datasource_driver-openaire2.0.json"))
|
||||
|
|
@ -52,7 +52,7 @@ public class MergeGraphSparkJobTest {
|
|||
.getClassid());
|
||||
assertEquals(
|
||||
"driver-openaire2.0",
|
||||
MergeGraphSparkJob
|
||||
MergeGraphTableSparkJob
|
||||
.mergeDatasource(
|
||||
d("datasource_driver-openaire2.0.json"),
|
||||
d("datasource_native.json"))
|
||||
|
|
@ -60,7 +60,7 @@ public class MergeGraphSparkJobTest {
|
|||
.getClassid());
|
||||
assertEquals(
|
||||
"openaire4.0",
|
||||
MergeGraphSparkJob
|
||||
MergeGraphTableSparkJob
|
||||
.mergeDatasource(
|
||||
d("datasource_notCompatible.json"),
|
||||
d("datasource_openaire4.0.json"))
|
||||
|
|
@ -68,7 +68,7 @@ public class MergeGraphSparkJobTest {
|
|||
.getClassid());
|
||||
assertEquals(
|
||||
"notCompatible",
|
||||
MergeGraphSparkJob
|
||||
MergeGraphTableSparkJob
|
||||
.mergeDatasource(
|
||||
d("datasource_notCompatible.json"),
|
||||
d("datasource_UNKNOWN.json"))
|
||||
|
|
@ -0,0 +1,99 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.raw;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.List;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest;
|
||||
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
public class GenerateEntitiesApplicationTest {
|
||||
|
||||
@Mock
|
||||
private ISLookUpService isLookUpService;
|
||||
|
||||
@Mock
|
||||
private VocabularyGroup vocs;
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() throws IOException, ISLookUpException {
|
||||
|
||||
lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
|
||||
lenient()
|
||||
.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
|
||||
.thenReturn(synonyms());
|
||||
|
||||
vocs = VocabularyGroup.loadVocsFromIS(isLookUpService);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testMergeResult() throws IOException {
|
||||
Result publication = getResult("oaf_record.xml", Publication.class);
|
||||
Result dataset = getResult("odf_dataset.xml", Dataset.class);
|
||||
Result software = getResult("odf_software.xml", Software.class);
|
||||
Result orp = getResult("oaf_orp.xml", OtherResearchProduct.class);
|
||||
|
||||
verifyMerge(publication, dataset, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
|
||||
verifyMerge(dataset, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
|
||||
|
||||
verifyMerge(publication, software, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
|
||||
verifyMerge(software, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
|
||||
|
||||
verifyMerge(publication, orp, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
|
||||
verifyMerge(orp, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
|
||||
|
||||
verifyMerge(dataset, software, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID);
|
||||
verifyMerge(software, dataset, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID);
|
||||
|
||||
verifyMerge(dataset, orp, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID);
|
||||
verifyMerge(orp, dataset, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID);
|
||||
|
||||
verifyMerge(software, orp, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID);
|
||||
verifyMerge(orp, software, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID);
|
||||
}
|
||||
|
||||
protected <T extends Result> void verifyMerge(Result publication, Result dataset, Class<T> clazz,
|
||||
String resultType) {
|
||||
final Result merge = OafMapperUtils.mergeResults(publication, dataset);
|
||||
assertTrue(clazz.isAssignableFrom(merge.getClass()));
|
||||
assertEquals(resultType, merge.getResulttype().getClassid());
|
||||
}
|
||||
|
||||
protected <T extends Result> Result getResult(String xmlFileName, Class<T> clazz) throws IOException {
|
||||
final String xml = IOUtils.toString(getClass().getResourceAsStream(xmlFileName));
|
||||
return new OdfToOafMapper(vocs, false)
|
||||
.processMdRecord(xml)
|
||||
.stream()
|
||||
.filter(s -> clazz.isAssignableFrom(s.getClass()))
|
||||
.map(s -> (Result) s)
|
||||
.findFirst()
|
||||
.get();
|
||||
}
|
||||
|
||||
private List<String> vocs() throws IOException {
|
||||
return IOUtils
|
||||
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"));
|
||||
}
|
||||
|
||||
private List<String> synonyms() throws IOException {
|
||||
return IOUtils
|
||||
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue