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fixing issue on previous implementation

This commit is contained in:
Miriam Baglioni 2020-11-24 14:44:53 +01:00
parent 7e940f1991
commit b9b6bdb2e6
2 changed files with 53 additions and 21 deletions
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55
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java
View File

@ -9,10 +9,7 @@ import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -22,6 +19,7 @@ import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
@ -69,11 +67,12 @@ public class SparkDumpFunderResults implements Serializable {
});
}
private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, String relationPath) {
private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath,
String relationPath) {
Dataset<Relation> relation = Utils
.readPath(spark, relationPath + "/relation", Relation.class)
.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
.filter("dataInfo.deletedbyinference = false and relClass = 'isProducedBy'");
Dataset<CommunityResult> result = Utils
.readPath(spark, inputPath + "/publication", CommunityResult.class)
@ -81,18 +80,40 @@ public class SparkDumpFunderResults implements Serializable {
.union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class))
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
result
.joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner")
.map((MapFunction<Tuple2<CommunityResult, Relation>, FunderResults>) value -> {
FunderResults res = (FunderResults) value._1();
res.setFunder_id(value._2().getSource().substring(3, 15));
return res;
}, Encoders.bean(FunderResults.class))
.write()
.partitionBy("funder_id")
.mode(SaveMode.Overwrite)
.json(outputPath);
List<String> funderList = relation
.select("target")
.map((MapFunction<Row, String>) value -> value.getString(0).substring(0, 15), Encoders.STRING())
.distinct()
.collectAsList();
// Dataset<CommunityResult> results = result
// .joinWith(relation, result.col("id").equalTo(relation.col("target")), "inner")
// .map((MapFunction<Tuple2<CommunityResult, Relation>, CommunityResult>) value -> {
// return value._1();
// }, Encoders.bean(CommunityResult.class));
funderList.forEach(funder -> writeFunderResult(funder, result, outputPath));
}
private static void writeFunderResult(String funder, Dataset<CommunityResult> results, String outputPath) {
results.map((MapFunction<CommunityResult, CommunityResult>) r -> {
if (!Optional.ofNullable(r.getProjects()).isPresent()) {
return null;
}
for (Project p : r.getProjects()) {
if (p.getId().startsWith(funder)) {
return r;
}
}
return null;
}, Encoders.bean(CommunityResult.class))
.filter(Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/" + funder);
}
}

19
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java
View File

@ -10,6 +10,7 @@ import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
@ -70,15 +71,25 @@ public class SparkResultLinkedToProject implements Serializable {
private static <R extends Result> void writeResultsLikedToProjects(SparkSession spark, Class<R> inputClazz,
String inputPath, String outputPath, String relationPath) {
Dataset<R> results = Utils.readPath(spark, inputPath, inputClazz);
Dataset<R> results = Utils
.readPath(spark, inputPath, inputClazz)
.filter("dataInfo.deletedbyinference = false and datainfo.invisible = false");
Dataset<Relation> relations = Utils
.readPath(spark, relationPath, Relation.class)
.filter("dataInfo.deletedbyinference = false and relClass = 'produces'");
.filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'");
relations
.joinWith(
results, relations.col("target").equalTo(results.col("id")),
results, relations.col("source").equalTo(results.col("id")),
"inner")
.map((MapFunction<Tuple2<Relation, R>, R>) t2 -> t2._2(), Encoders.bean(inputClazz))
.groupByKey(
(MapFunction<Tuple2<Relation, R>, String>) value -> value
._2()
.getId(),
Encoders.STRING())
.mapGroups((MapGroupsFunction<String, Tuple2<Relation, R>, R>) (k, it) -> {
return it.next()._2();
}, Encoders.bean(inputClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")