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no need to filter relations in CreateRelatedEntitiesJob_phase1; replaced 'left outer' join with 'left' join in CreateRelatedEntitiesJob_phase2; cleanup;

This commit is contained in:
Claudio Atzori 2020-11-12 09:22:59 +01:00
parent e3d3481fb9
commit 822971f54f
4 changed files with 9 additions and 100 deletions
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91
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java
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@ -1,91 +0,0 @@
package eu.dnetlib.dhp.oa.provision;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.expressions.Aggregator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.provision.model.*;
import scala.Tuple2;
import scala.collection.JavaConverters;
import scala.collection.Seq;
/**
* AdjacencyListBuilderJob: given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the
* result as JoinedEntity
*/
public class AdjacencyListBuilderJob {
private static final Logger log = LoggerFactory.getLogger(AdjacencyListBuilderJob.class);
public static final int MAX_LINKS = 100;
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
AdjacencyListBuilderJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ProvisionModelSupport.getModelClasses());
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
createAdjacencyListsKryo(spark, inputPath, outputPath);
});
}
private static void createAdjacencyListsKryo(
SparkSession spark, String inputPath, String outputPath) {
log.info("Reading joined entities from: {}", inputPath);
final List<String> paths = HdfsSupport
.listFiles(inputPath, spark.sparkContext().hadoopConfiguration());
log.info("Found paths: {}", String.join(",", paths));
}
private static Seq<String> toSeq(List<String> list) {
return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq();
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
}

1
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java
View File

@ -92,7 +92,6 @@ public class CreateRelatedEntitiesJob_phase1 {
String outputPath) {
Dataset<Tuple2<String, Relation>> relsByTarget = readPathRelation(spark, inputRelationsPath)
.filter("dataInfo.deletedbyinference == false")
.map(
(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(r.getTarget(),
r),

4
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java
View File

@ -105,7 +105,7 @@ public class CreateRelatedEntitiesJob_phase2 {
TypedColumn<JoinedEntity, JoinedEntity> aggregator = new AdjacencyListAggregator().toColumn();
entities
.joinWith(relatedEntities, entities.col("_1").equalTo(relatedEntities.col("_1")), "left_outer")
.joinWith(relatedEntities, entities.col("_1").equalTo(relatedEntities.col("_1")), "left")
.map((MapFunction<Tuple2<Tuple2<String, E>, Tuple2<String, RelatedEntityWrapper>>, JoinedEntity>) value -> {
JoinedEntity je = new JoinedEntity(value._1()._2());
Optional
@ -114,7 +114,6 @@ public class CreateRelatedEntitiesJob_phase2 {
.ifPresent(r -> je.getLinks().add(r));
return je;
}, Encoders.kryo(JoinedEntity.class))
.filter(filterEmptyEntityFn())
.groupByKey(
(MapFunction<JoinedEntity, String>) value -> value.getEntity().getId(),
Encoders.STRING())
@ -122,7 +121,6 @@ public class CreateRelatedEntitiesJob_phase2 {
.map(
(MapFunction<Tuple2<String, JoinedEntity>, JoinedEntity>) value -> value._2(),
Encoders.kryo(JoinedEntity.class))
.filter(filterEmptyEntityFn())
.write()
.mode(SaveMode.Overwrite)
.parquet(outputPath);

13
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java
View File

@ -3,8 +3,10 @@ package eu.dnetlib.dhp.oa.provision;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.*;
import java.util.function.Supplier;
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;
@ -15,8 +17,10 @@ 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.rdd.RDD;
import org.apache.spark.sql.*;
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;
@ -24,7 +28,6 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterables;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;