forked from D-Net/dnet-hadoop
SparkDedupTest updated and organization dump fixed
This commit is contained in:
miconis
parent
4da13e4570
commit
1102e32462
|
|
@ -1,29 +1,37 @@
|
|||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Paths;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
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.function.PairFunction;
|
||||
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.*;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.Mockito;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
|
|
@ -38,183 +46,127 @@ public class SparkDedupTest implements Serializable {
|
|||
private static String testGraphBasePath;
|
||||
private static String testOutputBasePath;
|
||||
private static String testDedupGraphBasePath;
|
||||
private static final String testActionSetId = "test-orchestrator";
|
||||
private final static String testActionSetId = "test-orchestrator";
|
||||
|
||||
@BeforeAll
|
||||
private static void cleanUp() throws IOException, URISyntaxException {
|
||||
|
||||
testGraphBasePath =
|
||||
Paths.get(
|
||||
SparkDedupTest.class
|
||||
.getResource("/eu/dnetlib/dhp/dedup/entities")
|
||||
.toURI())
|
||||
.toFile()
|
||||
.getAbsolutePath();
|
||||
testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath();
|
||||
|
||||
testOutputBasePath =
|
||||
createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
testDedupGraphBasePath =
|
||||
createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString();
|
||||
testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-").toAbsolutePath().toString();
|
||||
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
|
||||
spark =
|
||||
SparkSession.builder()
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(SparkCreateSimRels.class.getSimpleName())
|
||||
.master("local[*]")
|
||||
.config(new SparkConf())
|
||||
.getOrCreate();
|
||||
|
||||
jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
}
|
||||
|
||||
@BeforeEach
|
||||
private void setUp() throws IOException, ISLookUpException {
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
|
||||
.thenReturn(
|
||||
IOUtils.toString(
|
||||
SparkDedupTest.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
|
||||
lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
|
||||
.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
|
||||
.thenReturn(
|
||||
IOUtils.toString(
|
||||
SparkDedupTest.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
|
||||
lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
|
||||
.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
|
||||
|
||||
lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
|
||||
.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
|
||||
|
||||
lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
|
||||
.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
|
||||
.thenReturn(
|
||||
IOUtils.toString(
|
||||
SparkDedupTest.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(1)
|
||||
public void createSimRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser =
|
||||
new ArgumentApplicationParser(
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils.toString(
|
||||
SparkCreateSimRels.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
|
||||
parser.parseArgument(
|
||||
new String[] {
|
||||
"-mt", "local[*]",
|
||||
SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
|
||||
parser.parseArgument(new String[]{
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-la", "lookupurl",
|
||||
"-w", testOutputBasePath
|
||||
});
|
||||
"-w", testOutputBasePath});
|
||||
|
||||
new SparkCreateSimRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_simrel =
|
||||
spark.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
|
||||
.count();
|
||||
long pubs_simrel =
|
||||
spark.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
|
||||
.count();
|
||||
long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count();
|
||||
long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count();
|
||||
long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count();
|
||||
|
||||
assertEquals(3288, orgs_simrel);
|
||||
assertEquals(3432, orgs_simrel);
|
||||
assertEquals(7260, pubs_simrel);
|
||||
assertEquals(344, sw_simrel);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(2)
|
||||
public void createMergeRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser =
|
||||
new ArgumentApplicationParser(
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils.toString(
|
||||
SparkCreateMergeRels.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
|
||||
parser.parseArgument(
|
||||
new String[] {
|
||||
"-mt", "local[*]",
|
||||
SparkCreateMergeRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
|
||||
parser.parseArgument(new String[]{
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-la", "lookupurl",
|
||||
"-w", testOutputBasePath
|
||||
});
|
||||
"-w", testOutputBasePath});
|
||||
|
||||
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_mergerel =
|
||||
spark.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
||||
.count();
|
||||
long pubs_mergerel =
|
||||
spark.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
|
||||
.count();
|
||||
long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count();
|
||||
long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count();
|
||||
long sw_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel").count();
|
||||
|
||||
assertEquals(1244, orgs_mergerel);
|
||||
assertEquals(1276, orgs_mergerel);
|
||||
assertEquals(1460, pubs_mergerel);
|
||||
assertEquals(288, sw_mergerel);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(3)
|
||||
public void createDedupRecordTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser =
|
||||
new ArgumentApplicationParser(
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils.toString(
|
||||
SparkCreateDedupRecord.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
|
||||
parser.parseArgument(
|
||||
new String[] {
|
||||
"-mt", "local[*]",
|
||||
SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
|
||||
parser.parseArgument(new String[]{
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-la", "lookupurl",
|
||||
"-w", testOutputBasePath
|
||||
});
|
||||
"-w", testOutputBasePath});
|
||||
|
||||
new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_deduprecord =
|
||||
jsc.textFile(
|
||||
testOutputBasePath
|
||||
+ "/"
|
||||
+ testActionSetId
|
||||
+ "/organization_deduprecord")
|
||||
.count();
|
||||
long pubs_deduprecord =
|
||||
jsc.textFile(
|
||||
testOutputBasePath
|
||||
+ "/"
|
||||
+ testActionSetId
|
||||
+ "/publication_deduprecord")
|
||||
.count();
|
||||
long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count();
|
||||
long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count();
|
||||
long sw_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord").count();
|
||||
|
||||
assertEquals(82, orgs_deduprecord);
|
||||
assertEquals(66, pubs_deduprecord);
|
||||
assertEquals(51, sw_deduprecord);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(4)
|
||||
public void updateEntityTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser =
|
||||
new ArgumentApplicationParser(
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils.toString(
|
||||
SparkUpdateEntity.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
|
||||
parser.parseArgument(
|
||||
new String[] {
|
||||
"-mt", "local[*]",
|
||||
SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
|
||||
parser.parseArgument(new String[]{
|
||||
"-i", testGraphBasePath,
|
||||
"-w", testOutputBasePath,
|
||||
"-o", testDedupGraphBasePath
|
||||
|
|
@ -224,38 +176,34 @@ public class SparkDedupTest implements Serializable {
|
|||
|
||||
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 mergedOrgs =
|
||||
spark.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
long mergedOrgs = spark
|
||||
.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class))
|
||||
.where("relClass=='merges'")
|
||||
.javaRDD()
|
||||
.map(Relation::getTarget)
|
||||
.distinct()
|
||||
.count();
|
||||
.distinct().count();
|
||||
|
||||
long mergedPubs =
|
||||
spark.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
long mergedPubs = spark
|
||||
.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").as(Encoders.bean(Relation.class))
|
||||
.where("relClass=='merges'")
|
||||
.javaRDD()
|
||||
.map(Relation::getTarget)
|
||||
.distinct()
|
||||
.count();
|
||||
.distinct().count();
|
||||
|
||||
assertEquals(897, publications);
|
||||
assertEquals(831, publications);
|
||||
assertEquals(835, organizations);
|
||||
assertEquals(100, projects);
|
||||
assertEquals(100, datasource);
|
||||
assertEquals(200, softwares);
|
||||
|
||||
long deletedOrgs =
|
||||
jsc.textFile(testDedupGraphBasePath + "/organization")
|
||||
.filter(this::isDeletedByInference)
|
||||
.count();
|
||||
long deletedPubs =
|
||||
jsc.textFile(testDedupGraphBasePath + "/publication")
|
||||
.filter(this::isDeletedByInference)
|
||||
.count();
|
||||
long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization")
|
||||
.filter(this::isDeletedByInference).count();
|
||||
long deletedPubs = jsc.textFile(testDedupGraphBasePath + "/publication")
|
||||
.filter(this::isDeletedByInference).count();
|
||||
|
||||
assertEquals(mergedOrgs, deletedOrgs);
|
||||
assertEquals(mergedPubs, deletedPubs);
|
||||
|
|
@ -265,14 +213,10 @@ public class SparkDedupTest implements Serializable {
|
|||
@Order(5)
|
||||
public void propagateRelationTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser =
|
||||
new ArgumentApplicationParser(
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils.toString(
|
||||
SparkPropagateRelation.class.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
|
||||
parser.parseArgument(
|
||||
new String[] {
|
||||
"-mt", "local[*]",
|
||||
SparkPropagateRelation.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
|
||||
parser.parseArgument(new String[]{
|
||||
"-i", testGraphBasePath,
|
||||
"-w", testOutputBasePath,
|
||||
"-o", testDedupGraphBasePath
|
||||
|
|
@ -283,6 +227,28 @@ public class SparkDedupTest implements Serializable {
|
|||
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
||||
|
||||
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
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
Loading…
Reference in New Issue