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removed kryo encoding

This commit is contained in:
Michele Artini 2020-06-18 14:09:58 +02:00
parent 8d2b199dd2
commit 61634fbfe0
3 changed files with 34 additions and 23 deletions
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49
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java
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@ -28,8 +28,11 @@ import eu.dnetlib.dhp.broker.oa.util.EventGroup;
import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultAggregator; import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultAggregator;
import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup; import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.OpenaireBrokerResultAggregator; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.OpenaireBrokerResultAggregator;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedEntityFactory; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedEntityFactory;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication;
import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Publication;
@ -74,8 +77,8 @@ public class GenerateEventsApplication {
log.info("dedupConfigProfileId: {}", dedupConfigProfileId); log.info("dedupConfigProfileId: {}", dedupConfigProfileId);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); // conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(BrokerConstants.getModelClasses()); // conf.registerKryoClasses(BrokerConstants.getModelClasses());
// TODO UNCOMMENT // TODO UNCOMMENT
// final DedupConfig dedupConfig = loadDedupConfig(isLookupUrl, dedupConfigProfileId); // final DedupConfig dedupConfig = loadDedupConfig(isLookupUrl, dedupConfigProfileId);
@ -85,17 +88,24 @@ public class GenerateEventsApplication {
removeOutputDir(spark, eventsPath); removeOutputDir(spark, eventsPath);
// TODO UNCOMMENT // TODO REMOVE THIS
spark expandResultsWithRelations(spark, graphPath, Publication.class)
.emptyDataset(Encoders.kryo(Event.class))
.union(generateEvents(spark, graphPath, Publication.class, dedupConfig))
// .union(generateEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class, dedupConfig))
// .union(generateEvents(spark, graphPath, Software.class, dedupConfig))
// .union(generateEvents(spark, graphPath, OtherResearchProduct.class, dedupConfig))
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip") .option("compression", "gzip")
.json(eventsPath); .json(eventsPath);
// TODO UNCOMMENT THIS
// spark
// .emptyDataset(Encoders.bean(Event.class))
// .union(generateEvents(spark, graphPath, Publication.class, dedupConfig))
// .union(generateEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class, dedupConfig))
// .union(generateEvents(spark, graphPath, Software.class, dedupConfig))
// .union(generateEvents(spark, graphPath, OtherResearchProduct.class, dedupConfig))
// .write()
// .mode(SaveMode.Overwrite)
// .option("compression", "gzip")
// .json(eventsPath);
}); });
} }
@ -123,12 +133,12 @@ public class GenerateEventsApplication {
.groupByKey( .groupByKey(
(MapFunction<Tuple2<OpenaireBrokerResult, Relation>, String>) t -> t._2.getTarget(), Encoders.STRING()) (MapFunction<Tuple2<OpenaireBrokerResult, Relation>, String>) t -> t._2.getTarget(), Encoders.STRING())
.agg(aggr) .agg(aggr)
.map((MapFunction<Tuple2<String, ResultGroup>, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class)) .map((MapFunction<Tuple2<String, ResultGroup>, ResultGroup>) t -> t._2, Encoders.bean(ResultGroup.class))
.filter(ResultGroup::isValid) .filter(ResultGroup::isValid)
.map( .map(
(MapFunction<ResultGroup, EventGroup>) g -> EventFinder.generateEvents(g, dedupConfig), (MapFunction<ResultGroup, EventGroup>) g -> EventFinder.generateEvents(g, dedupConfig),
Encoders.kryo(EventGroup.class)) Encoders.bean(EventGroup.class))
.flatMap(group -> group.getData().iterator(), Encoders.kryo(Event.class)); .flatMap(group -> group.getData().iterator(), Encoders.bean(Event.class));
} }
private static <SRC extends Result> Dataset<OpenaireBrokerResult> expandResultsWithRelations( private static <SRC extends Result> Dataset<OpenaireBrokerResult> expandResultsWithRelations(
@ -147,15 +157,16 @@ public class GenerateEventsApplication {
.cache(); .cache();
final Dataset<OpenaireBrokerResult> r0 = readPath( final Dataset<OpenaireBrokerResult> r0 = readPath(
spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class) spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass)
.filter(r -> r.getDataInfo().getDeletedbyinference()) .filter(r -> r.getDataInfo().getDeletedbyinference())
.map(ConversionUtils::oafResultToBrokerResult, Encoders.kryo(OpenaireBrokerResult.class)); .map(ConversionUtils::oafResultToBrokerResult, Encoders.bean(OpenaireBrokerResult.class));
final Dataset<OpenaireBrokerResult> r1 = join(r0, rels, relatedEntities(projects, rels, RelatedProject.class)); final Dataset<OpenaireBrokerResult> r1 = join(r0, rels, relatedEntities(projects, rels, RelatedProject.class));
final Dataset<OpenaireBrokerResult> r2 = join(r1, rels, relatedEntities(softwares, rels, RelatedProject.class)); final Dataset<OpenaireBrokerResult> r2 = join(
final Dataset<OpenaireBrokerResult> r3 = join(r2, rels, relatedEntities(datasets, rels, RelatedProject.class)); r1, rels, relatedEntities(softwares, rels, RelatedSoftware.class));
final Dataset<OpenaireBrokerResult> r3 = join(r2, rels, relatedEntities(datasets, rels, RelatedDataset.class));
final Dataset<OpenaireBrokerResult> r4 = join( final Dataset<OpenaireBrokerResult> r4 = join(
r3, rels, relatedEntities(publications, rels, RelatedProject.class)); r3, rels, relatedEntities(publications, rels, RelatedPublication.class));
; ;
return r4; return r4;
@ -168,7 +179,7 @@ public class GenerateEventsApplication {
.joinWith(targets, targets.col("id").equalTo(rels.col("target")), "inner") .joinWith(targets, targets.col("id").equalTo(rels.col("target")), "inner")
.map( .map(
t -> RelatedEntityFactory.newRelatedEntity(t._1.getSource(), t._1.getRelType(), t._2, clazz), t -> RelatedEntityFactory.newRelatedEntity(t._1.getSource(), t._1.getRelType(), t._2, clazz),
Encoders.kryo(clazz)); Encoders.bean(clazz));
} }
private static <T> Dataset<OpenaireBrokerResult> join(final Dataset<OpenaireBrokerResult> sources, private static <T> Dataset<OpenaireBrokerResult> join(final Dataset<OpenaireBrokerResult> sources,
@ -184,7 +195,7 @@ public class GenerateEventsApplication {
.groupByKey( .groupByKey(
(MapFunction<Tuple2<OpenaireBrokerResult, T>, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) (MapFunction<Tuple2<OpenaireBrokerResult, T>, String>) t -> t._1.getOpenaireId(), Encoders.STRING())
.agg(aggr) .agg(aggr)
.map(t -> t._2, Encoders.kryo(OpenaireBrokerResult.class)); .map(t -> t._2, Encoders.bean(OpenaireBrokerResult.class));
} }

4
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java
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@ -38,13 +38,13 @@ public class ResultAggregator extends Aggregator<Tuple2<OpenaireBrokerResult, Re
@Override @Override
public Encoder<ResultGroup> bufferEncoder() { public Encoder<ResultGroup> bufferEncoder() {
return Encoders.kryo(ResultGroup.class); return Encoders.bean(ResultGroup.class);
} }
@Override @Override
public Encoder<ResultGroup> outputEncoder() { public Encoder<ResultGroup> outputEncoder() {
return Encoders.kryo(ResultGroup.class); return Encoders.bean(ResultGroup.class);
} }

4
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OpenaireBrokerResultAggregator.java
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@ -58,12 +58,12 @@ public class OpenaireBrokerResultAggregator<T>
@Override @Override
public Encoder<OpenaireBrokerResult> bufferEncoder() { public Encoder<OpenaireBrokerResult> bufferEncoder() {
return Encoders.kryo(OpenaireBrokerResult.class); return Encoders.bean(OpenaireBrokerResult.class);
} }
@Override @Override
public Encoder<OpenaireBrokerResult> outputEncoder() { public Encoder<OpenaireBrokerResult> outputEncoder() {
return Encoders.kryo(OpenaireBrokerResult.class); return Encoders.bean(OpenaireBrokerResult.class);
} }
} }