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added the isTest checkpoint

This commit is contained in:
Miriam Baglioni 2020-04-16 10:53:48 +02:00
parent c28333d43f
commit 53f418098b
1 changed files with 9 additions and 11 deletions
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20
dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob2.java
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@ -8,6 +8,7 @@ import eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
@ -58,9 +59,6 @@ public class SparkResultToOrganizationFromIstRepoJob2 {
final String alreadylinked = parser.get("alreadyLinkedPath");
log.info("alreadyLinkedPath: {}", alreadylinked);
final String resultorganizationsetpath = parser.get("resultOrganizationsetPath");
log.info("resultOrganizationsetPath: {}", resultorganizationsetpath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
@ -93,9 +91,6 @@ public class SparkResultToOrganizationFromIstRepoJob2 {
writeUpdates, saveGraph);
});
}
private static void execPropagation(SparkSession spark, String datasourceorganization, String alreadylinked, String inputPath,
@ -122,17 +117,20 @@ public class SparkResultToOrganizationFromIstRepoJob2 {
.read()
.textFile(alreadylinked)
.map(value -> OBJECT_MAPPER.readValue(value, ResultOrganizationSet.class),
Encoders.bean(ResultOrganizationSet.class)), potentialUpdates);
Encoders.bean(ResultOrganizationSet.class)), potentialUpdates)
.toJavaRDD()
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
.saveAsTextFile(outputPath , GzipCodec.class);
}
}
private static Dataset<Relation> getNewRelations(Dataset<ResultOrganizationSet> alreadyLinked, Dataset<ResultOrganizationSet> potentialUpdates) {
return potentialUpdates
.joinWith(alreadyLinked, potentialUpdates.col("resultId")
.equalTo(alreadyLinked.col("resultId")), "left_outer")
.flatMap((FlatMapFunction<Tuple2<ResultOrganizationSet, ResultOrganizationSet>, Relation>) value -> {
return potentialUpdates
.joinWith(alreadyLinked, potentialUpdates.col("resultId")
.equalTo(alreadyLinked.col("resultId")), "left_outer").flatMap((FlatMapFunction<Tuple2<ResultOrganizationSet, ResultOrganizationSet>, Relation>) value -> {
List<Relation> new_relations = new ArrayList<>();
ResultOrganizationSet potential_update = value._1();
Optional<ResultOrganizationSet> already_linked = Optional.ofNullable(value._2());