andreas.czerniak
/
BrBETA_dnet-hadoop
forked from D-Net/dnet-hadoop
1
1
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity

dedup testing

This commit is contained in:
miconis 2020-04-01 18:48:31 +02:00
parent 7061d07727
commit 9802bcb9fe
4 changed files with 179 additions and 105 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
dhp-workflows/dhp-dedup-openaire/pom.xml
View File

@ -90,6 +90,12 @@
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
</dependencies>

100
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java
View File

@ -5,7 +5,9 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.util.MapDocumentUtil;
@ -17,12 +19,18 @@ 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.Encoders;
import org.apache.spark.sql.SparkSession;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
import scala.Tuple2;
import java.io.Serializable;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
public class SparkCreateSimRels implements Serializable {
@ -51,35 +59,38 @@ public class SparkCreateSimRels implements Serializable {
System.out.println(String.format("actionSetId: '%s'", actionSetId));
System.out.println(String.format("workingPath: '%s'", workingPath));
try (SparkSession spark = getSparkSession(parser)) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
List<DedupConfig> configurations = getConfigurations(isLookUpUrl, actionSetId);
System.out.println("configurations = " + configurations.size());
//for each dedup configuration
for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) {
final String entity = dedupConf.getWf().getEntityType();
final String subEntity = dedupConf.getWf().getSubEntityValue();
JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
.mapToPair(s -> {
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
return new Tuple2<>(d.getIdentifier(), d);
});
//create blocks for deduplication
JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
//create relations by comparing only elements in the same group
final JavaPairRDD<String, String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
JavaRDD<Relation> relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity));
//save the simrel in the workingdir
spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class))
.write()
.mode("overwrite")
.save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity));
}
}
// try (SparkSession spark = getSparkSession(parser)) {
// final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
//
// //for each dedup configuration
// for (DedupConfig dedupConf: getConfigurations(isLookUpUrl, actionSetId)) {
// final String entity = dedupConf.getWf().getEntityType();
// final String subEntity = dedupConf.getWf().getSubEntityValue();
//
// JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
// .mapToPair((PairFunction<String, String, MapDocument>) s -> {
// MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
// return new Tuple2<String, MapDocument>(d.getIdentifier(), d);
// });
//
// //create blocks for deduplication
// JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
//
// //create relations by comparing only elements in the same group
// final JavaPairRDD<String, String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
//
// JavaRDD<Relation> relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity));
//
// //save the simrel in the workingdir
// spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class))
// .write()
// .mode("overwrite")
// .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity));
// }
// }
}
/**
@ -131,4 +142,37 @@ public class SparkCreateSimRels implements Serializable {
.getOrCreate();
}
public List<DedupConfig> getConfigurations(String isLookUpUrl, String orchestrator) throws ISLookUpException, DocumentException {
final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookUpUrl);
final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator);
String orchestratorProfile = isLookUpService.getResourceProfileByQuery(xquery);
final Document doc = new SAXReader().read(new StringReader(orchestratorProfile));
final String actionSetId = doc.valueOf("//DEDUPLICATION/ACTION_SET/@id");
final List<DedupConfig> configurations = new ArrayList<>();
for (final Object o : doc.selectNodes("//SCAN_SEQUENCE/SCAN")) {
configurations.add(loadConfig(isLookUpService, actionSetId, o));
}
return configurations;
}
public DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o)
throws ISLookUpException {
final Element s = (Element) o;
final String configProfileId = s.attributeValue("id");
final String conf =
isLookUpService.getResourceProfileByQuery(String.format(
"for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()",
configProfileId));
final DedupConfig dedupConfig = DedupConfig.load(conf);
dedupConfig.getWf().setConfigurationId(actionSetId);
return dedupConfig;
}
}

77
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkCreateDedupTest.java
View File

@ -1,77 +0,0 @@
package eu.dnetlib.dhp.oa.dedup.dedup;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.dedup.SparkCreateConnectedComponent;
import eu.dnetlib.dhp.oa.dedup.SparkCreateDedupRecord;
import eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import java.io.IOException;
public class SparkCreateDedupTest {
String configuration;
String entity = "organization";
@BeforeEach
public void setUp() throws IOException {
// configuration = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dedup/conf/org.curr.conf.json"));
configuration = "";
}
@Disabled("must be parametrized to run locally")
public void createSimRelsTest() throws Exception {
SparkCreateSimRels.main(new String[]{
"-mt", "local[*]",
"-i", "/Users/miconis/dumps",
"-o", "/tmp/dedup/rawset_test",
"-asi", "dedup-similarity-result-levenstein",
"-la", "lookupurl",
"-w", "workingPath"
});
}
@Disabled("must be parametrized to run locally")
public void createCCTest() throws Exception {
SparkCreateConnectedComponent.main(new String[]{
"-mt", "local[*]",
"-s", "/Users/miconis/dumps",
"-e", entity,
"-c", ArgumentApplicationParser.compressArgument(configuration),
"-t", "/tmp/dedup",
});
}
@Disabled("must be parametrized to run locally")
public void dedupRecordTest() throws Exception {
SparkCreateDedupRecord.main(new String[]{
"-mt", "local[*]",
"-s", "/Users/miconis/dumps",
"-e", entity,
"-c", ArgumentApplicationParser.compressArgument(configuration),
"-d", "/tmp/dedup",
});
}
@Disabled("must be parametrized to run locally")
public void printConfiguration() throws Exception {
System.out.println(ArgumentApplicationParser.compressArgument(configuration));
}
@Disabled("must be parametrized to run locally")
public void testHashCode() {
final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f";
final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46";
final HashFunction hashFunction = Hashing.murmur3_128();
System.out.println(s1.hashCode());
System.out.println(hashFunction.hashString(s1).asLong());
System.out.println(s2.hashCode());
System.out.println(hashFunction.hashString(s2).asLong());
}
}

101
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/dedup/SparkDedupTest.java Normal file
View File

@ -0,0 +1,101 @@
package eu.dnetlib.dhp.oa.dedup.dedup;
import com.google.common.collect.Lists;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.dedup.SparkCreateConnectedComponent;
import eu.dnetlib.dhp.oa.dedup.SparkCreateDedupRecord;
import eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.pace.config.DedupConfig;
import org.apache.commons.io.IOUtils;
import org.dom4j.DocumentException;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import org.junit.runner.RunWith;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.List;
@RunWith(MockitoJUnitRunner.Silent.class)
public class SparkDedupTest {
@Mock
SparkCreateSimRels sparkCreateSimRels;
public List<DedupConfig> prepareConfigurations() throws IOException {
return Lists.newArrayList(
DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))),
DedupConfig.load(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")))
);
}
@Before
public void setUp() throws IOException, ISLookUpException, DocumentException {
when(sparkCreateSimRels.getConfigurations(anyString(), anyString())).thenReturn(prepareConfigurations());
}
@Test
public void createSimRelsTest() throws Exception {
SparkCreateSimRels.main(new String[]{
"-mt", "local[*]",
"-i", "/Users/miconis/dumps",
"-asi", "dedup-similarity-result-levenstein",
"-la", "lookupurl",
"-w", "workingPath"
});
}
// @Disabled("must be parametrized to run locally")
// public void createCCTest() throws Exception {
//
// SparkCreateConnectedComponent.main(new String[]{
// "-mt", "local[*]",
// "-s", "/Users/miconis/dumps",
// "-e", entity,
// "-c", ArgumentApplicationParser.compressArgument(configuration),
// "-t", "/tmp/dedup",
// });
// }
//
// @Disabled("must be parametrized to run locally")
// public void dedupRecordTest() throws Exception {
// SparkCreateDedupRecord.main(new String[]{
// "-mt", "local[*]",
// "-s", "/Users/miconis/dumps",
// "-e", entity,
// "-c", ArgumentApplicationParser.compressArgument(configuration),
// "-d", "/tmp/dedup",
// });
// }
//
// @Disabled("must be parametrized to run locally")
// public void printConfiguration() throws Exception {
// System.out.println(ArgumentApplicationParser.compressArgument(configuration));
// }
@Disabled("must be parametrized to run locally")
public void testHashCode() {
final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f";
final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46";
final HashFunction hashFunction = Hashing.murmur3_128();
System.out.println(s1.hashCode());
System.out.println(hashFunction.hashString(s1).asLong());
System.out.println(s2.hashCode());
System.out.println(hashFunction.hashString(s2).asLong());
}
}