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fixed behaviour of DedupRecordFactory

This commit is contained in:
Claudio Atzori 2020-04-20 18:44:06 +02:00
parent ede1af3d85
commit eb8a020859
3 changed files with 239 additions and 139 deletions
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45
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
View File

@ -5,29 +5,29 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.config.DedupConfig;
import java.util.Collection;
import java.util.Iterator;
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.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
public class DedupRecordFactory {
private static final Logger log = LoggerFactory.getLogger(DedupRecordFactory.class);
protected static final ObjectMapper OBJECT_MAPPER =
new com.fasterxml.jackson.databind.ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
public static <T extends OafEntity> Dataset<T> createDedupRecord(
final SparkSession spark,
final String mergeRelsInputPath,
final String entitiesInputPath,
final Class<T> clazz,
final DedupConfig dedupConf) {
final Class<T> clazz) {
long ts = System.currentTimeMillis();
@ -54,40 +54,39 @@ public class DedupRecordFactory {
r -> new Tuple2<>(r.getSource(), r.getTarget()),
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
// <dedup_id, json_entity_merged>
return mergeRels
.joinWith(entities, mergeRels.col("_1").equalTo(entities.col("_1")), "left_outer")
.filter(
(FilterFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>>)
value -> value._2() != null)
.joinWith(entities, mergeRels.col("_2").equalTo(entities.col("_1")), "inner")
.map(
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, T>>, T>)
value -> value._2()._2(),
Encoders.kryo(clazz))
.groupByKey((MapFunction<T, String>) value -> value.getId(), Encoders.STRING())
(MapFunction<
Tuple2<Tuple2<String, String>, Tuple2<String, T>>,
Tuple2<String, T>>)
value -> new Tuple2<>(value._1()._1(), value._2()._2()),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
.groupByKey(
(MapFunction<Tuple2<String, T>, String>) entity -> entity._1(),
Encoders.STRING())
.mapGroups(
(MapGroupsFunction<String, T, T>)
(MapGroupsFunction<String, Tuple2<String, T>, T>)
(key, values) -> entityMerger(key, values, ts, clazz),
Encoders.bean(clazz));
}
private static <T extends OafEntity> T entityMerger(
String id, Iterator<T> entities, final long ts, Class<T> clazz) {
String id, Iterator<Tuple2<String, T>> entities, long ts, Class<T> clazz) {
try {
T entity = clazz.newInstance();
entity.setId(id);
if (entity.getDataInfo() == null) {
entity.setDataInfo(new DataInfo());
}
entity.getDataInfo().setTrust("0.9");
entity.setLastupdatetimestamp(ts);
final Collection<String> dates = Lists.newArrayList();
entities.forEachRemaining(
e -> {
entity.mergeFrom(e);
if (ModelSupport.isSubClass(e, Result.class)) {
Result r1 = (Result) e;
t -> {
T duplicate = t._2();
entity.mergeFrom(duplicate);
if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result r1 = (Result) duplicate;
Result er = (Result) entity;
er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));

2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
View File

@ -71,7 +71,7 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz, dedupConf)
DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz)
.map(
(MapFunction<OafEntity, String>)
value -> OBJECT_MAPPER.writeValueAsString(value),

245
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
View File

@ -1,10 +1,19 @@
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 eu.dnetlib.pace.util.MapDocumentUtil;
import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.net.URISyntaxException;
import java.nio.file.Paths;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -23,16 +32,6 @@ 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)
public class SparkDedupTest implements Serializable {
@ -46,65 +45,104 @@ public class SparkDedupTest implements Serializable {
private static String testGraphBasePath;
private static String testOutputBasePath;
private static String testDedupGraphBasePath;
private final static String testActionSetId = "test-orchestrator";
private static final String testActionSetId = "test-orchestrator";
@BeforeAll
private static void cleanUp() throws IOException, URISyntaxException {
public 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 {
public 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")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
.thenReturn(
IOUtils.toString(
SparkDedupTest.class.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/sw.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[]{
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 sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_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(3432, orgs_simrel);
assertEquals(7260, pubs_simrel);
@ -115,20 +153,33 @@ public class SparkDedupTest implements Serializable {
@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[]{
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 sw_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_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(1276, orgs_mergerel);
assertEquals(1460, pubs_mergerel);
@ -139,20 +190,38 @@ public class SparkDedupTest implements Serializable {
@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[]{
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 sw_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_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);
@ -163,10 +232,13 @@ public class SparkDedupTest implements Serializable {
@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[]{
SparkUpdateEntity.class.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
parser.parseArgument(
new String[] {
"-i", testGraphBasePath,
"-w", testOutputBasePath,
"-o", testDedupGraphBasePath
@ -180,19 +252,25 @@ public class SparkDedupTest implements Serializable {
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(831, publications);
assertEquals(835, organizations);
@ -200,10 +278,15 @@ public class SparkDedupTest implements Serializable {
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);
@ -213,10 +296,13 @@ 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[]{
SparkPropagateRelation.class.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
parser.parseArgument(
new String[] {
"-i", testGraphBasePath,
"-w", testOutputBasePath,
"-o", testDedupGraphBasePath
@ -228,20 +314,35 @@ public class SparkDedupTest implements Serializable {
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
// 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"));
.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("$.source", json), json))
JavaRDD<String> toCheck =
jsc.textFile(testDedupGraphBasePath + "/relation")
.mapToPair(
json ->
new Tuple2<>(
MapDocumentUtil.getJPathString("$.source", json),
json))
.join(mergedIds)
.map(t -> t._2()._1())
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
.mapToPair(
json ->
new Tuple2<>(
MapDocumentUtil.getJPathString("$.target", json),
json))
.join(mergedIds)
.map(t -> t._2()._1());