281 lines
14 KiB
Java
281 lines
14 KiB
Java
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package eu.dnetlib.dhp.broker.oa;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.List;
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import java.util.Map;
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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.tuple.Pair;
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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.JavaRDD;
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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.Column;
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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.Row;
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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.broker.model.Event;
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import eu.dnetlib.dhp.broker.model.EventFactory;
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import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsReferencedBy;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsRelatedTo;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsSupplementedBy;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsSupplementedTo;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetReferences;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedProjects.EnrichMissingProject;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedProjects.EnrichMoreProject;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsReferencedBy;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsRelatedTo;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedBy;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedTo;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationReferences;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAbstract;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAuthorOrcid;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingOpenAccess;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPid;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingSoftware;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingSubject;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreOpenAccess;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMorePid;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSoftware;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSubject;
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import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
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import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
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import eu.dnetlib.dhp.common.HdfsSupport;
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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.Result;
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import eu.dnetlib.dhp.schema.oaf.Software;
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public class GenerateEventsApplication {
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private static final Logger log = LoggerFactory.getLogger(GenerateEventsApplication.class);
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// Simple Matchers
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private static final UpdateMatcher<Result, ?> enrichMissingAbstract = new EnrichMissingAbstract();
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private static final UpdateMatcher<Result, ?> enrichMissingAuthorOrcid = new EnrichMissingAuthorOrcid();
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private static final UpdateMatcher<Result, ?> enrichMissingOpenAccess = new EnrichMissingOpenAccess();
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private static final UpdateMatcher<Result, ?> enrichMissingPid = new EnrichMissingPid();
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private static final UpdateMatcher<Result, ?> enrichMissingPublicationDate = new EnrichMissingPublicationDate();
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private static final UpdateMatcher<Result, ?> enrichMissingSubject = new EnrichMissingSubject();
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private static final UpdateMatcher<Result, ?> enrichMoreOpenAccess = new EnrichMoreOpenAccess();
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private static final UpdateMatcher<Result, ?> enrichMorePid = new EnrichMorePid();
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private static final UpdateMatcher<Result, ?> enrichMoreSubject = new EnrichMoreSubject();
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// Advanced matchers
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private static final UpdateMatcher<Pair<Result, List<Project>>, ?> enrichMissingProject = new EnrichMissingProject();
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private static final UpdateMatcher<Pair<Result, List<Project>>, ?> enrichMoreProject = new EnrichMoreProject();
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private static final UpdateMatcher<Pair<Result, List<Software>>, ?> enrichMissingSoftware = new EnrichMissingSoftware();
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private static final UpdateMatcher<Pair<Result, List<Software>>, ?> enrichMoreSoftware = new EnrichMoreSoftware();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMisissingPublicationIsRelatedTo = new EnrichMissingPublicationIsRelatedTo();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsReferencedBy = new EnrichMissingPublicationIsReferencedBy();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationReferences = new EnrichMissingPublicationReferences();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedTo = new EnrichMissingPublicationIsSupplementedTo();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedBy = new EnrichMissingPublicationIsSupplementedBy();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMisissingDatasetIsRelatedTo = new EnrichMissingDatasetIsRelatedTo();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsReferencedBy = new EnrichMissingDatasetIsReferencedBy();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetReferences = new EnrichMissingDatasetReferences();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedTo = new EnrichMissingDatasetIsSupplementedTo();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedBy = new EnrichMissingDatasetIsSupplementedBy();
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public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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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GenerateEventsApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json")));
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parser.parseArgument(args);
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final 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 graphPath = parser.get("graphPath");
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log.info("graphPath: {}", graphPath);
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final String eventsPath = parser.get("eventsPath");
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log.info("eventsPath: {}", eventsPath);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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removeOutputDir(spark, eventsPath);
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final JavaRDD<Event> eventsRdd = sc.emptyRDD();
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eventsRdd.union(generateSimpleEvents(spark, graphPath, Publication.class));
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eventsRdd.union(generateSimpleEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class));
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eventsRdd.union(generateSimpleEvents(spark, graphPath, Software.class));
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eventsRdd.union(generateSimpleEvents(spark, graphPath, OtherResearchProduct.class));
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eventsRdd.saveAsTextFile(eventsPath, GzipCodec.class);
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});
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}
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private static void removeOutputDir(final SparkSession spark, final String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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private static <R extends Result> JavaRDD<Event> generateSimpleEvents(final SparkSession spark,
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final String graphPath,
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final Class<R> resultClazz) {
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final Dataset<R> results = readPath(
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spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), resultClazz)
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.filter(r -> r.getDataInfo().getDeletedbyinference());
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final Dataset<Relation> rels = readPath(spark, graphPath + "/relation", Relation.class)
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.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
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final Column c = null; // TODO
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final Dataset<Row> aa = results
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.joinWith(rels, results.col("id").equalTo(rels.col("source")), "inner")
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.groupBy(rels.col("target"))
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.agg(c)
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.filter(x -> x.size() > 1)
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// generateSimpleEvents(...)
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// flatMap()
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// toRdd()
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;
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return null;
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}
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private List<Event> generateSimpleEvents(final Collection<Result> children) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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for (final Result target : children) {
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list.addAll(enrichMissingAbstract.searchUpdatesForRecord(target, children));
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list.addAll(enrichMissingAuthorOrcid.searchUpdatesForRecord(target, children));
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list.addAll(enrichMissingOpenAccess.searchUpdatesForRecord(target, children));
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list.addAll(enrichMissingPid.searchUpdatesForRecord(target, children));
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list.addAll(enrichMissingPublicationDate.searchUpdatesForRecord(target, children));
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list.addAll(enrichMissingSubject.searchUpdatesForRecord(target, children));
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list.addAll(enrichMoreOpenAccess.searchUpdatesForRecord(target, children));
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list.addAll(enrichMorePid.searchUpdatesForRecord(target, children));
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list.addAll(enrichMoreSubject.searchUpdatesForRecord(target, children));
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}
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return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
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}
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private List<Event> generateProjectsEvents(final Collection<Pair<Result, List<Project>>> childrenWithProjects) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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for (final Pair<Result, List<Project>> target : childrenWithProjects) {
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list.addAll(enrichMissingProject.searchUpdatesForRecord(target, childrenWithProjects));
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list.addAll(enrichMoreProject.searchUpdatesForRecord(target, childrenWithProjects));
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}
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return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
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}
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private List<Event> generateSoftwareEvents(final Collection<Pair<Result, List<Software>>> childrenWithSoftwares) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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for (final Pair<Result, List<Software>> target : childrenWithSoftwares) {
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list.addAll(enrichMissingSoftware.searchUpdatesForRecord(target, childrenWithSoftwares));
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list.addAll(enrichMoreSoftware.searchUpdatesForRecord(target, childrenWithSoftwares));
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}
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return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
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}
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private List<Event> generatePublicationRelatedEvents(final String relType,
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final Collection<Pair<Result, Map<String, List<Publication>>>> childrenWithRels) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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final List<Pair<Result, List<Publication>>> cleanedChildrens = childrenWithRels
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.stream()
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.filter(p -> p.getRight().containsKey(relType))
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.map(p -> Pair.of(p.getLeft(), p.getRight().get(relType)))
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.filter(p -> p.getRight().size() > 0)
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.collect(Collectors.toList());
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for (final Pair<Result, List<Publication>> target : cleanedChildrens) {
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if (relType.equals("isRelatedTo")) {
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list.addAll(enrichMisissingPublicationIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens));
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} else if (relType.equals("references")) {
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list.addAll(enrichMissingPublicationReferences.searchUpdatesForRecord(target, cleanedChildrens));
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} else if (relType.equals("isReferencedBy")) {
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list.addAll(enrichMissingPublicationIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens));
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} else if (relType.equals("isSupplementedTo")) {
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list.addAll(enrichMissingPublicationIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens));
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} else if (relType.equals("isSupplementedBy")) {
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list.addAll(enrichMissingPublicationIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens));
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}
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}
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return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
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}
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private List<Event> generateDatasetRelatedEvents(final String relType,
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final Collection<Pair<Result, Map<String, List<eu.dnetlib.dhp.schema.oaf.Dataset>>>> childrenWithRels) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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final List<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>> cleanedChildrens = childrenWithRels
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.stream()
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.filter(p -> p.getRight().containsKey(relType))
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.map(p -> Pair.of(p.getLeft(), p.getRight().get(relType)))
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.filter(p -> p.getRight().size() > 0)
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.collect(Collectors.toList());
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for (final Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>> target : cleanedChildrens) {
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if (relType.equals("isRelatedTo")) {
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list.addAll(enrichMisissingDatasetIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens));
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} else if (relType.equals("references")) {
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list.addAll(enrichMissingDatasetReferences.searchUpdatesForRecord(target, cleanedChildrens));
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} else if (relType.equals("isReferencedBy")) {
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list.addAll(enrichMissingDatasetIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens));
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} else if (relType.equals("isSupplementedTo")) {
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list.addAll(enrichMissingDatasetIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens));
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} else if (relType.equals("isSupplementedBy")) {
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list.addAll(enrichMissingDatasetIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens));
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}
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}
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return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
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}
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public static <R> Dataset<R> readPath(
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final SparkSession spark,
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final String inputPath,
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final Class<R> clazz) {
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return spark
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.read()
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.textFile(inputPath)
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.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
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}
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}
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