D-Net
/
dhp-graph-dump
4
0
Fork 0
Code Issues Pull Requests 1 Projects Releases Wiki Activity

[SKG-IF] fixing issue in deserialization

This commit is contained in:
Miriam Baglioni 2024-03-14 13:02:47 +01:00
parent b176bbef1d
commit 187b91a699
2 changed files with 23 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

30
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/filterentities/SelectConnectedEntities.java
View File

@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable; import java.io.Serializable;
import java.util.Arrays; import java.util.Arrays;
import java.util.Optional; import java.util.Optional;
import java.util.function.Predicate;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
@ -19,6 +20,9 @@ import org.apache.spark.sql.Dataset;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.skgif.EmitFromEntities; import eu.dnetlib.dhp.oa.graph.dump.skgif.EmitFromEntities;
import eu.dnetlib.dhp.oa.graph.dump.skgif.Utils; import eu.dnetlib.dhp.oa.graph.dump.skgif.Utils;
@ -71,9 +75,9 @@ public class SelectConnectedEntities implements Serializable {
private static <R extends Result> void selectConnectedEntities(SparkSession spark, String inputPath, private static <R extends Result> void selectConnectedEntities(SparkSession spark, String inputPath,
String filterPath, String filterPath,
String workingDir) { String workingDir) throws JsonProcessingException {
Dataset<Identifiers> resultIds = spark.emptyDataset(Encoders.bean(Identifiers.class)); Dataset<String> resultIds = spark.emptyDataset(Encoders.STRING());
for (EntityType entity : ModelSupport.entityTypes.keySet()) for (EntityType entity : ModelSupport.entityTypes.keySet())
if (ModelSupport.isResult(entity)) if (ModelSupport.isResult(entity))
resultIds = resultIds resultIds = resultIds
@ -81,8 +85,11 @@ public class SelectConnectedEntities implements Serializable {
spark spark
.read() .read()
.parquet(filterPath + entity.name() + "_ids") .parquet(filterPath + entity.name() + "_ids")
.as(Encoders.bean(Identifiers.class))); .select("id")
.as(Encoders.STRING()));
// log.info("Number of identifiers in the result {}", resultIds.count());
log.info("Deserialization of the first id {}", new ObjectMapper().writeValueAsString(resultIds.first()));
Dataset<Relation> relation = Utils Dataset<Relation> relation = Utils
.readPath(spark, inputPath + "relation", Relation.class) .readPath(spark, inputPath + "relation", Relation.class)
.filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference()); .filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference());
@ -104,17 +111,25 @@ public class SelectConnectedEntities implements Serializable {
// select relations having source in the set of identifiers selected for eosc // select relations having source in the set of identifiers selected for eosc
Dataset<Relation> resultSource = resultIds Dataset<Relation> resultSource = resultIds
.joinWith(relation, resultIds.col("id").equalTo(relation.col("source"))) .joinWith(relation, resultIds.col("_1").equalTo(relation.col("source")))
.map((MapFunction<Tuple2<Identifiers, Relation>, Relation>) t2 -> t2._2(), Encoders.bean(Relation.class)); .map((MapFunction<Tuple2<String, Relation>, Relation>) t2 -> t2._2(), Encoders.bean(Relation.class));
// write relations having source and target in the set // write relations having source and target in the set
resultIds resultIds
.joinWith(resultSource, resultIds.col("id").equalTo(resultSource.col("target"))) .joinWith(resultSource, resultIds.col("_1").equalTo(resultSource.col("target")))
.map((MapFunction<Tuple2<Identifiers, Relation>, Relation>) t2 -> t2._2(), Encoders.bean(Relation.class)) .map((MapFunction<Tuple2<String, Relation>, Relation>) t2 -> t2._2(), Encoders.bean(Relation.class))
.write() .write()
.option("compression", "gzip") .option("compression", "gzip")
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.json(workingDir + "relation"); .json(workingDir + "relation");
log
.info(
"Number of relations in the result {}", resultIds
.joinWith(resultSource, resultIds.col("id").equalTo(resultSource.col("target")))
.map(
(MapFunction<Tuple2<String, Relation>, Relation>) t2 -> t2._2(),
Encoders.bean(Relation.class))
.count());
// write relations between results and organizations // write relations between results and organizations
resultSource resultSource
@ -125,7 +140,6 @@ public class SelectConnectedEntities implements Serializable {
.option("compression", "gzip") .option("compression", "gzip")
.json(workingDir + "relation"); .json(workingDir + "relation");
// write relations between results and projects
resultSource resultSource
.joinWith(projects, resultSource.col("target").equalTo(projects.col("id"))) .joinWith(projects, resultSource.col("target").equalTo(projects.col("id")))
.map((MapFunction<Tuple2<Relation, Project>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class)) .map((MapFunction<Tuple2<Relation, Project>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class))

2
dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/skgif/oozie_app/workflow.xml
View File

@ -212,7 +212,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg> <arg>--sourcePath</arg><arg>${sourcePath}</arg>
<!-- <arg>&#45;&#45;workingDir</arg><arg>${workingDir}/graph/</arg>--> <!-- <arg>&#45;&#45;workingDir</arg><arg>${workingDir}/graph/</arg>-->
<arg>--workingDir</arg><arg>${nameNode}/user/miriam.baglioni/oa/graph/dump/temp/graph/</arg> <arg>--workingDir</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/graph/</arg>
<arg>--filterPath</arg><arg>${filterPath}</arg> <arg>--filterPath</arg><arg>${filterPath}</arg>
</spark> </spark>
<!-- <ok to="emit_from_result"/>--> <!-- <ok to="emit_from_result"/>-->