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PrepareRelationsJob rewritten to use Spark Dataframe API and Windowing functions

This commit is contained in:
Giambattista Bloisi 2024-05-07 15:44:33 +02:00
parent 26363060ed
commit 711048ceed
1 changed files with 38 additions and 152 deletions
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190
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java
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@ -1,43 +1,31 @@
package eu.dnetlib.dhp.oa.provision;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.HashSet;
import java.util.Optional;
import java.util.PriorityQueue;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.Function;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.expressions.Aggregator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Joiner;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterables;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
import eu.dnetlib.dhp.oa.provision.model.SortableRelationKey;
import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner;
import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.expressions.Window;
import org.apache.spark.sql.expressions.WindowSpec;
import org.apache.spark.sql.functions;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.HashSet;
import java.util.Optional;
import java.util.Set;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static org.apache.spark.sql.functions.col;
/**
* PrepareRelationsJob prunes the relationships: only consider relationships that are not virtually deleted
@ -130,130 +118,28 @@ public class PrepareRelationsJob {
private static void prepareRelationsRDD(SparkSession spark, String inputRelationsPath, String outputPath,
Set<String> relationFilter, int sourceMaxRelations, int targetMaxRelations, int relPartitions) {
JavaRDD<Relation> rels = readPathRelationRDD(spark, inputRelationsPath)
.filter(rel -> !(rel.getSource().startsWith("unresolved") || rel.getTarget().startsWith("unresolved")))
.filter(rel -> !rel.getDataInfo().getDeletedbyinference())
.filter(rel -> !relationFilter.contains(StringUtils.lowerCase(rel.getRelClass())));
WindowSpec source_w = Window
.partitionBy("source", "subRelType")
.orderBy(col("target").desc_nulls_last());
JavaRDD<Relation> pruned = pruneRels(
pruneRels(
rels,
sourceMaxRelations, relPartitions, (Function<Relation, String>) Relation::getSource),
targetMaxRelations, relPartitions, (Function<Relation, String>) Relation::getTarget);
spark
.createDataset(pruned.rdd(), Encoders.bean(Relation.class))
.repartition(relPartitions)
.write()
.mode(SaveMode.Overwrite)
.parquet(outputPath);
}
WindowSpec target_w = Window
.partitionBy("target", "subRelType")
.orderBy(col("source").desc_nulls_last());
private static JavaRDD<Relation> pruneRels(JavaRDD<Relation> rels, int maxRelations,
int relPartitions, Function<Relation, String> idFn) {
return rels
.mapToPair(r -> new Tuple2<>(SortableRelationKey.create(r, idFn.call(r)), r))
.repartitionAndSortWithinPartitions(new RelationPartitioner(relPartitions))
.groupBy(Tuple2::_1)
.map(Tuple2::_2)
.map(t -> Iterables.limit(t, maxRelations))
.flatMap(Iterable::iterator)
.map(Tuple2::_2);
}
// experimental
private static void prepareRelationsDataset(
SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter, int maxRelations,
int relPartitions) {
spark
.read()
.textFile(inputRelationsPath)
.repartition(relPartitions)
.map(
(MapFunction<String, Relation>) s -> OBJECT_MAPPER.readValue(s, Relation.class),
Encoders.kryo(Relation.class))
.filter((FilterFunction<Relation>) rel -> !rel.getDataInfo().getDeletedbyinference())
.filter((FilterFunction<Relation>) rel -> !relationFilter.contains(rel.getRelClass()))
.groupByKey(
(MapFunction<Relation, String>) Relation::getSource,
Encoders.STRING())
.agg(new RelationAggregator(maxRelations).toColumn())
.flatMap(
(FlatMapFunction<Tuple2<String, RelationList>, Relation>) t -> Iterables
.limit(t._2().getRelations(), maxRelations)
.iterator(),
Encoders.bean(Relation.class))
.repartition(relPartitions)
.write()
.mode(SaveMode.Overwrite)
.parquet(outputPath);
}
public static class RelationAggregator
extends Aggregator<Relation, RelationList, RelationList> {
private final int maxRelations;
public RelationAggregator(int maxRelations) {
this.maxRelations = maxRelations;
}
@Override
public RelationList zero() {
return new RelationList();
}
@Override
public RelationList reduce(RelationList b, Relation a) {
b.getRelations().add(a);
return getSortableRelationList(b);
}
@Override
public RelationList merge(RelationList b1, RelationList b2) {
b1.getRelations().addAll(b2.getRelations());
return getSortableRelationList(b1);
}
@Override
public RelationList finish(RelationList r) {
return getSortableRelationList(r);
}
private RelationList getSortableRelationList(RelationList b1) {
RelationList sr = new RelationList();
sr
.setRelations(
b1
.getRelations()
.stream()
.limit(maxRelations)
.collect(Collectors.toCollection(() -> new PriorityQueue<>(new RelationComparator()))));
return sr;
}
@Override
public Encoder<RelationList> bufferEncoder() {
return Encoders.kryo(RelationList.class);
}
@Override
public Encoder<RelationList> outputEncoder() {
return Encoders.kryo(RelationList.class);
}
}
/**
* Reads a JavaRDD of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text
* file,
*
* @param spark
* @param inputPath
* @return the JavaRDD<SortableRelation> containing all the relationships
*/
private static JavaRDD<Relation> readPathRelationRDD(
SparkSession spark, final String inputPath) {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
return sc.textFile(inputPath).map(s -> OBJECT_MAPPER.readValue(s, Relation.class));
spark.read().schema(Encoders.bean(Relation.class).schema()).json(inputRelationsPath)
.where("source NOT LIKE 'unresolved%' AND target NOT LIKE 'unresolved%'")
.where("datainfo.deletedbyinference != true")
.where(relationFilter.isEmpty() ? "" : "lower(relClass) NOT IN ("+ Joiner.on(',').join(relationFilter) +")")
.withColumn("source_w_pos", functions.row_number().over(source_w))
.where("source_w_pos < " + sourceMaxRelations )
.drop("source_w_pos")
.withColumn("target_w_pos", functions.row_number().over(target_w))
.where("target_w_pos < " + targetMaxRelations)
.drop( "target_w_pos")
.coalesce(relPartitions)
.write()
.mode(SaveMode.Overwrite)
.parquet(outputPath);
}
private static void removeOutputDir(SparkSession spark, String path) {