minor changes
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@ -17,7 +17,6 @@ import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.apache.spark.sql.sources.In;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@ -31,7 +30,6 @@ 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.provision.model.SortableRelation;
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import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner;
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import scala.Int;
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import scala.Tuple2;
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/**
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@ -112,26 +110,74 @@ public class PrepareRelationsJob {
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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prepareRelationsRDDFromPaths(
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prepareRelationsRDD(
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spark, inputRelationsPath, outputPath, relationFilter, relPartitions, maxRelations);
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});
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}
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private static void prepareRelationsFromPaths(
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SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter) {
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/**
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* Dataset based implementation that prepares the graph relations by limiting the number of outgoing links and
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* filtering the relation types according to the given criteria.
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*
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* @param spark the spark session
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* @param inputRelationsPath source path for the graph relations
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* @param outputPath output path for the processed relations
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* @param relationFilter set of relation filters applied to the `relClass` field
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* @param maxRelations maximum number of allowed outgoing edges
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*/
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private static void prepareRelations(
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SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter,
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int maxRelations) {
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readPathRelation(spark, inputRelationsPath)
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.filter("dataInfo.deletedbyinference == false")
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.filter((FilterFunction<SortableRelation>) rel -> !relationFilter.contains(rel.getRelClass()))
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.groupByKey(
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(MapFunction<SortableRelation, String>) value -> value.getSource(), Encoders.STRING())
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.flatMapGroups(
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(FlatMapGroupsFunction<String, SortableRelation, SortableRelation>) (key, values) -> Iterators
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.limit(values, MAX_RELS),
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.limit(values, maxRelations),
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Encoders.bean(SortableRelation.class))
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.write()
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.mode(SaveMode.Overwrite)
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.parquet(outputPath);
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}
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/**
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* RDD based implementation that prepares the graph relations by limiting the number of outgoing links and filtering
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* the relation types according to the given criteria. Moreover, outgoing links kept within the given limit are
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* prioritized according to the weights indicated in eu.dnetlib.dhp.oa.provision.model.SortableRelation.
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*
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* @param spark the spark session
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* @param inputRelationsPath source path for the graph relations
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* @param outputPath output path for the processed relations
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* @param relationFilter set of relation filters applied to the `relClass` field
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* @param maxRelations maximum number of allowed outgoing edges
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*/
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// TODO work in progress
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private static void prepareRelationsRDD(
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SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter, int relPartitions,
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int maxRelations) {
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JavaRDD<SortableRelation> rels = readPathRelationRDD(spark, inputRelationsPath).repartition(relPartitions);
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RelationPartitioner partitioner = new RelationPartitioner(rels.getNumPartitions());
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// only consider those that are not virtually deleted
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RDD<SortableRelation> d = rels
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.filter(rel -> !rel.getDataInfo().getDeletedbyinference())
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.filter(rel -> !relationFilter.contains(rel.getRelClass()))
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.mapToPair(
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(PairFunction<SortableRelation, SortableRelation, SortableRelation>) rel -> new Tuple2<>(rel, rel))
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.groupByKey(partitioner)
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.map(group -> Iterables.limit(group._2(), maxRelations))
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.flatMap(group -> group.iterator())
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.rdd();
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spark
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.createDataset(d, Encoders.bean(SortableRelation.class))
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.write()
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.mode(SaveMode.Overwrite)
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.parquet(outputPath);
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}
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/**
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* Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text
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* file,
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@ -150,30 +196,6 @@ public class PrepareRelationsJob {
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Encoders.bean(SortableRelation.class));
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}
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// TODO work in progress
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private static void prepareRelationsRDDFromPaths(
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SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter, int relPartitions,
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int maxRelations) {
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JavaRDD<SortableRelation> rels = readPathRelationRDD(spark, inputRelationsPath).repartition(relPartitions);
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// only consider those that are not virtually deleted
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RDD<SortableRelation> d = rels
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.filter(rel -> !rel.getDataInfo().getDeletedbyinference())
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.filter(rel -> !relationFilter.contains(rel.getRelClass()))
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.mapToPair(
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(PairFunction<SortableRelation, SortableRelation, SortableRelation>) rel -> new Tuple2<>(rel, rel))
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.groupByKey(new RelationPartitioner(rels.getNumPartitions()))
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.map(group -> Iterables.limit(group._2(), maxRelations))
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.flatMap(group -> group.iterator())
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.rdd();
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spark
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.createDataset(d, Encoders.bean(SortableRelation.class))
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.write()
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.mode(SaveMode.Overwrite)
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.parquet(outputPath);
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}
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private static JavaRDD<SortableRelation> readPathRelationRDD(
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SparkSession spark, final String inputPath) {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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@ -80,6 +80,11 @@
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</description>
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</property>
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<property>
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<name>sparkNetworkTimeout</name>
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<description>configures spark.network.timeout</description>
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</property>
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</parameters>
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<global>
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@ -357,7 +362,7 @@
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<arg>--inputGraphRootPath</arg><arg>${inputGraphRootPath}</arg>
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<arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
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<arg>--outputPath</arg><arg>${workingDir}/join_entities</arg>
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<arg>--numPartitions</arg><arg>12000</arg>
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<arg>--numPartitions</arg><arg>24000</arg>
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</spark>
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<ok to="adjancency_lists"/>
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<error to="Kill"/>
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@ -381,7 +386,7 @@
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--conf spark.sql.shuffle.partitions=7680
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--conf spark.network.timeout=${sparkNetworkTimeout}
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</spark-opts>
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<arg>--inputPath</arg> <arg>${workingDir}/join_entities</arg>
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<arg>--inputPath</arg><arg>${workingDir}/join_entities</arg>
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<arg>--outputPath</arg><arg>${workingDir}/joined</arg>
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</spark>
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<ok to="convert_to_xml"/>
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