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implementation of the deletedbyinference test in propagating relations

This commit is contained in:
miconis 2020-04-17 10:40:21 +02:00
parent cb0952428e
commit 418cf94642
2 changed files with 30 additions and 0 deletions
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2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
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@ -83,12 +83,14 @@ public class SparkPropagateRelation extends AbstractSparkAction {
.textFile(relationPath) .textFile(relationPath)
.map(patchRelFn(), Encoders.bean(Relation.class)); .map(patchRelFn(), Encoders.bean(Relation.class));
//change raw ids with dedup ids
Dataset<Relation> newRels = Dataset<Relation> newRels =
processDataset( processDataset(
processDataset(rels, mergedIds, FieldType.SOURCE, getFixRelFn(FieldType.SOURCE)), processDataset(rels, mergedIds, FieldType.SOURCE, getFixRelFn(FieldType.SOURCE)),
mergedIds, FieldType.TARGET, getFixRelFn(FieldType.TARGET)) mergedIds, FieldType.TARGET, getFixRelFn(FieldType.TARGET))
.filter(SparkPropagateRelation::containsDedup); .filter(SparkPropagateRelation::containsDedup);
//update deletedbyinference
Dataset<Relation> updated = processDataset( Dataset<Relation> updated = processDataset(
processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()), processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()),
mergedIds, FieldType.TARGET, getDeletedFn()); mergedIds, FieldType.TARGET, getDeletedFn());

28
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
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@ -4,17 +4,24 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.util.MapDocumentUtil;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*; import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
import org.mockito.Mockito; import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import scala.Tuple2;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
@ -211,6 +218,27 @@ public class SparkDedupTest implements Serializable {
assertEquals(826, relations); assertEquals(826, relations);
//check deletedbyinference
final Dataset<Relation> mergeRels = spark.read().load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*")).as(Encoders.bean(Relation.class));
final JavaPairRDD<String, String> mergedIds = mergeRels
.where("relClass == 'merges'")
.select(mergeRels.col("target"))
.distinct()
.toJavaRDD()
.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
JavaRDD<String> toCheck = jsc.textFile(testDedupGraphBasePath + "/relation")
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
.join(mergedIds)
.map(t -> t._2()._1())
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
.join(mergedIds)
.map(t -> t._2()._1());
long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
long updated = toCheck.count();
assertEquals(updated, deletedbyinference);
} }
@AfterAll @AfterAll