forked from antonis.lempesis/dnet-hadoop
reverted behaviour of the cleaning workflow: grouping entities by ID will be managed differently
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parent
e43ab07af6
commit
33bae02451
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@ -1,206 +0,0 @@
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package eu.dnetlib.dhp.oa.graph.clean;
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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.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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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.*;
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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.Configuration;
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import com.jayway.jsonpath.DocumentContext;
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import com.jayway.jsonpath.JsonPath;
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import com.jayway.jsonpath.Option;
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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 GroupEntitiesAndRelationsSparkJob {
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private static final Logger log = LoggerFactory.getLogger(GroupEntitiesAndRelationsSparkJob.class);
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private final static String ID_JPATH = "$.id";
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private final static String SOURCE_JPATH = "$.source";
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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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GroupEntitiesAndRelationsSparkJob.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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groupEntitiesAndRelations(spark, graphInputPath, outputPath);
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});
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}
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private static void groupEntitiesAndRelations(
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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(listPaths(inputPath, sc)))
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.map((MapFunction<String, Oaf>) s -> parseOaf(s), Encoders.kryo(Oaf.class))
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.filter((FilterFunction<Oaf>) oaf -> StringUtils.isNotBlank(ModelSupport.idFn().apply(oaf)))
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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(
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(MapFunction<Tuple2<String, Oaf>, String>) t -> t._2().getClass().getName() +
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"|" + OBJECT_MAPPER.writeValueAsString(t._2()),
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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(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 Oaf parseOaf(String s) {
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DocumentContext dc = JsonPath
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.parse(s, Configuration.defaultConfiguration().addOptions(Option.SUPPRESS_EXCEPTIONS));
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final String id = dc.read(ID_JPATH);
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if (StringUtils.isNotBlank(id)) {
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String prefix = StringUtils.substringBefore(id, "|");
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switch (prefix) {
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case "10":
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return parse(s, Datasource.class);
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case "20":
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return parse(s, Organization.class);
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case "40":
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return parse(s, Project.class);
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case "50":
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String resultType = dc.read("$.resulttype.classid");
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switch (resultType) {
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case "publication":
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return parse(s, Publication.class);
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case "dataset":
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return parse(s, eu.dnetlib.dhp.schema.oaf.Dataset.class);
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case "software":
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return parse(s, Software.class);
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case "other":
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return parse(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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} else {
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String source = dc.read(SOURCE_JPATH);
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if (StringUtils.isNotBlank(source)) {
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return parse(s, Relation.class);
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} else {
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throw new IllegalArgumentException(String.format("invalid oaf: '%s'", s));
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}
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}
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}
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private static <T extends Oaf> Oaf parse(String s, Class<T> clazz) {
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try {
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return OBJECT_MAPPER.readValue(s, clazz);
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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> listPaths(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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.collect(Collectors.toList());
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}
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}
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@ -50,36 +50,12 @@
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</property>
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</parameters>
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<start to="group_entities"/>
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<start to="fork_clean_graph"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="group_entities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>group graph entities and relations</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.GroupEntitiesAndRelationsSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--graphInputPath</arg><arg>${graphInputPath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/grouped_entities</arg>
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</spark>
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<ok to="fork_clean_graph"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_clean_graph">
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<path start="clean_publication"/>
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<path start="clean_dataset"/>
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@ -108,7 +84,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--inputPath</arg><arg>${graphInputPath}/publication</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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@ -134,7 +110,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--inputPath</arg><arg>${graphInputPath}/dataset</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/dataset</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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@ -160,7 +136,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--inputPath</arg><arg>${graphInputPath}/otherresearchproduct</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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@ -186,7 +162,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--inputPath</arg><arg>${graphInputPath}/software</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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@ -212,7 +188,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--inputPath</arg><arg>${graphInputPath}/datasource</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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@ -238,7 +214,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--inputPath</arg><arg>${graphInputPath}/organization</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/organization</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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@ -264,7 +240,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--inputPath</arg><arg>${graphInputPath}/project</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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@ -290,7 +266,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--inputPath</arg><arg>${graphInputPath}/relation</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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