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recert file SparkDedupTest.java

This commit is contained in:
Michele Artini 2021-05-04 10:26:14 +02:00
parent 49910aedca
commit f4bd2b5619
1 changed files with 131 additions and 119 deletions
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172
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
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@ -12,6 +12,7 @@ import java.io.IOException;
import java.io.Serializable;
import java.net.URISyntaxException;
import java.nio.file.Paths;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
@ -26,13 +27,7 @@ import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.MethodOrderer;
import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestMethodOrder;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.Mockito;
@ -102,7 +97,8 @@ public class SparkDedupTest implements Serializable {
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
@ -110,7 +106,8 @@ public class SparkDedupTest implements Serializable {
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
@ -118,7 +115,8 @@ public class SparkDedupTest implements Serializable {
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
@ -126,7 +124,8 @@ public class SparkDedupTest implements Serializable {
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset")))
@ -134,7 +133,8 @@ public class SparkDedupTest implements Serializable {
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct")))
@ -142,21 +142,24 @@ public class SparkDedupTest implements Serializable {
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")));
}
@Test
@Order(1)
public void createSimRelsTest() throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateSimRels.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
parser
.parseArgument(new String[] {
.parseArgument(
new String[] {
"-i", testGraphBasePath,
"-asi", testActionSetId,
"-la", "lookupurl",
@ -166,27 +169,27 @@ public class SparkDedupTest implements Serializable {
new SparkCreateSimRels(parser, spark).run(isLookUpService);
final long orgs_simrel = spark
long orgs_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
.count();
final long pubs_simrel = spark
long pubs_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication"))
.count();
final long sw_simrel = spark
long sw_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software"))
.count();
final long ds_simrel = spark
long ds_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset"))
.count();
final long orp_simrel = spark
long orp_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct"))
.count();
@ -202,14 +205,16 @@ public class SparkDedupTest implements Serializable {
@Order(2)
public void cutMergeRelsTest() throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateMergeRels.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
parser
.parseArgument(new String[] {
.parseArgument(
new String[] {
"-i",
testGraphBasePath,
"-asi",
@ -224,7 +229,7 @@ public class SparkDedupTest implements Serializable {
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
final long orgs_mergerel = spark
long orgs_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
.as(Encoders.bean(Relation.class))
@ -235,7 +240,7 @@ public class SparkDedupTest implements Serializable {
.where("cnt > 3")
.count();
final long pubs_mergerel = spark
long pubs_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
.as(Encoders.bean(Relation.class))
@ -245,7 +250,7 @@ public class SparkDedupTest implements Serializable {
.select("source", "cnt")
.where("cnt > 3")
.count();
final long sw_mergerel = spark
long sw_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
.as(Encoders.bean(Relation.class))
@ -256,7 +261,7 @@ public class SparkDedupTest implements Serializable {
.where("cnt > 3")
.count();
final long ds_mergerel = spark
long ds_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
.as(Encoders.bean(Relation.class))
@ -267,7 +272,7 @@ public class SparkDedupTest implements Serializable {
.where("cnt > 3")
.count();
final long orp_mergerel = spark
long orp_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
.as(Encoders.bean(Relation.class))
@ -296,14 +301,16 @@ public class SparkDedupTest implements Serializable {
@Order(3)
public void createMergeRelsTest() throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateMergeRels.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
parser
.parseArgument(new String[] {
.parseArgument(
new String[] {
"-i",
testGraphBasePath,
"-asi",
@ -316,24 +323,24 @@ public class SparkDedupTest implements Serializable {
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
final long orgs_mergerel = spark
long orgs_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
.count();
final long pubs_mergerel = spark
long pubs_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
.count();
final long sw_mergerel = spark
long sw_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
.count();
final long ds_mergerel = spark
long ds_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
.count();
final long orp_mergerel = spark
long orp_mergerel = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
.count();
@ -350,13 +357,15 @@ public class SparkDedupTest implements Serializable {
@Order(4)
public void createDedupRecordTest() throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateDedupRecord.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
parser
.parseArgument(new String[] {
.parseArgument(
new String[] {
"-i",
testGraphBasePath,
"-asi",
@ -369,20 +378,19 @@ public class SparkDedupTest implements Serializable {
new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
final long orgs_deduprecord = jsc
long orgs_deduprecord = jsc
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord")
.count();
final long pubs_deduprecord = jsc
long pubs_deduprecord = jsc
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord")
.count();
final long sw_deduprecord = jsc
long sw_deduprecord = jsc
.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
.count();
final long ds_deduprecord = jsc
.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_deduprecord")
.count();
final long orp_deduprecord = jsc
.textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord")
long ds_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_deduprecord").count();
long orp_deduprecord = jsc
.textFile(
testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord")
.count();
assertEquals(85, orgs_deduprecord);
@ -396,27 +404,29 @@ public class SparkDedupTest implements Serializable {
@Order(5)
public void updateEntityTest() throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkUpdateEntity.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
parser
.parseArgument(new String[] {
.parseArgument(
new String[] {
"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
});
new SparkUpdateEntity(parser, spark).run(isLookUpService);
final long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
final long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
final long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
final long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
final long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
final long dataset = jsc.textFile(testDedupGraphBasePath + "/dataset").count();
final long otherresearchproduct = jsc.textFile(testDedupGraphBasePath + "/otherresearchproduct").count();
long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
long dataset = jsc.textFile(testDedupGraphBasePath + "/dataset").count();
long otherresearchproduct = jsc.textFile(testDedupGraphBasePath + "/otherresearchproduct").count();
final long mergedOrgs = spark
long mergedOrgs = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
.as(Encoders.bean(Relation.class))
@ -426,7 +436,7 @@ public class SparkDedupTest implements Serializable {
.distinct()
.count();
final long mergedPubs = spark
long mergedPubs = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
.as(Encoders.bean(Relation.class))
@ -436,7 +446,7 @@ public class SparkDedupTest implements Serializable {
.distinct()
.count();
final long mergedSw = spark
long mergedSw = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
.as(Encoders.bean(Relation.class))
@ -446,7 +456,7 @@ public class SparkDedupTest implements Serializable {
.distinct()
.count();
final long mergedDs = spark
long mergedDs = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
.as(Encoders.bean(Relation.class))
@ -456,7 +466,7 @@ public class SparkDedupTest implements Serializable {
.distinct()
.count();
final long mergedOrp = spark
long mergedOrp = spark
.read()
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
.as(Encoders.bean(Relation.class))
@ -474,27 +484,27 @@ public class SparkDedupTest implements Serializable {
assertEquals(389, dataset);
assertEquals(517, otherresearchproduct);
final long deletedOrgs = jsc
long deletedOrgs = jsc
.textFile(testDedupGraphBasePath + "/organization")
.filter(this::isDeletedByInference)
.count();
final long deletedPubs = jsc
long deletedPubs = jsc
.textFile(testDedupGraphBasePath + "/publication")
.filter(this::isDeletedByInference)
.count();
final long deletedSw = jsc
long deletedSw = jsc
.textFile(testDedupGraphBasePath + "/software")
.filter(this::isDeletedByInference)
.count();
final long deletedDs = jsc
long deletedDs = jsc
.textFile(testDedupGraphBasePath + "/dataset")
.filter(this::isDeletedByInference)
.count();
final long deletedOrp = jsc
long deletedOrp = jsc
.textFile(testDedupGraphBasePath + "/otherresearchproduct")
.filter(this::isDeletedByInference)
.count();
@ -510,19 +520,21 @@ public class SparkDedupTest implements Serializable {
@Order(6)
public void propagateRelationTest() throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkPropagateRelation.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
parser
.parseArgument(new String[] {
.parseArgument(
new String[] {
"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
});
new SparkPropagateRelation(parser, spark).run(isLookUpService);
final long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
assertEquals(4862, relations);
@ -536,9 +548,10 @@ public class SparkDedupTest implements Serializable {
.select(mergeRels.col("target"))
.distinct()
.toJavaRDD()
.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
.mapToPair(
(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
final JavaRDD<String> toCheck = jsc
JavaRDD<String> toCheck = jsc
.textFile(testDedupGraphBasePath + "/relation")
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
.join(mergedIds)
@ -547,8 +560,8 @@ public class SparkDedupTest implements Serializable {
.join(mergedIds)
.map(t -> t._2()._1());
final long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
final long updated = toCheck.count();
long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
long updated = toCheck.count();
assertEquals(updated, deletedbyinference);
}
@ -560,8 +573,8 @@ public class SparkDedupTest implements Serializable {
testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2);
}
private void testUniqueness(final String path, final int expected_total, final int expected_unique) {
final Dataset<Relation> rel = spark
private void testUniqueness(String path, int expected_total, int expected_unique) {
Dataset<Relation> rel = spark
.read()
.textFile(getClass().getResource(path).getPath())
.map(
@ -578,8 +591,7 @@ public class SparkDedupTest implements Serializable {
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
}
public boolean isDeletedByInference(final String s) {
public boolean isDeletedByInference(String s) {
return s.contains("\"deletedbyinference\":true");
}
}