forked from D-Net/dnet-hadoop
further implementation of tests for the deduplication of each entity. publication dump added, empty entity files created
This commit is contained in:
miconis
parent
56fbe689f0
commit
0be2e72be5
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@ -20,7 +20,6 @@ public class MergeAuthorTest {
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public void setUp() throws Exception {
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public void setUp() throws Exception {
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final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/json/authors_merge.json"));
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final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/json/authors_merge.json"));
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publicationsToMerge = Arrays.asList(json.split("\n")).stream().map(s-> {
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publicationsToMerge = Arrays.asList(json.split("\n")).stream().map(s-> {
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try {
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try {
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return mapper.readValue(s, Publication.class);
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return mapper.readValue(s, Publication.class);
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@ -1,13 +1,14 @@
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package eu.dnetlib.dhp.oa.dedup;
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package eu.dnetlib.dhp.oa.dedup;
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import com.google.common.hash.HashFunction;
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import com.google.common.hash.Hashing;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.*;
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import org.junit.jupiter.api.*;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.junit.jupiter.api.extension.ExtendWith;
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@ -17,20 +18,22 @@ import org.mockito.junit.jupiter.MockitoExtension;
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import java.io.File;
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import java.io.File;
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import java.io.IOException;
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import java.io.IOException;
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import java.io.Serializable;
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import java.net.URISyntaxException;
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import java.net.URISyntaxException;
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import java.nio.file.Paths;
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import java.nio.file.Paths;
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import static org.mockito.Mockito.when;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.mockito.Mockito.lenient;
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@ExtendWith(MockitoExtension.class)
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@ExtendWith(MockitoExtension.class)
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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public class SparkDedupTest {
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public class SparkDedupTest implements Serializable {
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@Mock
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@Mock(serializable = true)
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ISLookUpService isLookUpService;
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ISLookUpService isLookUpService;
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private SparkSession spark;
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private static SparkSession spark;
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private static JavaSparkContext jsc;
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private static String testGraphBasePath;
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private static String testGraphBasePath;
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private final static String testOutputBasePath = "/tmp/test_dedup_workflow";
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private final static String testOutputBasePath = "/tmp/test_dedup_workflow";
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@ -43,10 +46,6 @@ public class SparkDedupTest {
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testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath();
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testGraphBasePath = Paths.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI()).toFile().getAbsolutePath();
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FileUtils.deleteDirectory(new File(testOutputBasePath));
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FileUtils.deleteDirectory(new File(testOutputBasePath));
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}
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@BeforeEach
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private void setUp() throws IOException, ISLookUpException {
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spark = SparkSession
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spark = SparkSession
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.builder()
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.builder()
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@ -55,13 +54,20 @@ public class SparkDedupTest {
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.config(new SparkConf())
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.config(new SparkConf())
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.getOrCreate();
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.getOrCreate();
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when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
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jsc = new JavaSparkContext(spark.sparkContext());
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}
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@BeforeEach
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private void setUp() throws IOException, ISLookUpException {
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lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
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when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
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lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
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when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
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lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
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.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
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}
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}
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@ -85,11 +91,8 @@ public class SparkDedupTest {
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long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count();
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long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count();
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long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count();
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long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count();
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System.out.println("pubs_simrel = " + pubs_simrel);
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assertEquals(3288, orgs_simrel);
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System.out.println("orgs_simrel = " + orgs_simrel);
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assertEquals(7260, pubs_simrel);
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// assertEquals(918, orgs_simrel);
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// assertEquals(0, pubs_simrel);
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}
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}
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@Test
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@Test
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@ -111,16 +114,14 @@ public class SparkDedupTest {
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long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count();
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long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count();
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long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count();
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long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count();
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System.out.println("pubs_mergerel = " + pubs_mergerel);
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assertEquals(1244, orgs_mergerel);
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System.out.println("orgs_mergerel = " + orgs_mergerel);
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assertEquals(1460, pubs_mergerel);
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// assertEquals(458, orgs_mergerel);
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// assertEquals(0, pubs_mergerel);
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}
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}
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@Test
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@Test
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@Order(3)
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@Order(3)
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public void dedupRecordTest() throws Exception {
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public void createDedupRecordTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(
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IOUtils.toString(
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@ -134,13 +135,11 @@ public class SparkDedupTest {
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new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
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new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
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long orgs_deduprecord = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count();
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long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count();
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long pubs_deduprecord = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count();
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long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count();
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System.out.println("pubs_deduprecord = " + pubs_deduprecord);
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assertEquals(82, orgs_deduprecord);
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System.out.println("pubs_deduprecord = " + orgs_deduprecord);
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assertEquals(66, pubs_deduprecord);
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// assertEquals(458, orgs_deduprecord);
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// assertEquals(0, pubs_deduprecord);
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}
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}
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@Test
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@Test
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@ -159,12 +158,35 @@ public class SparkDedupTest {
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new SparkUpdateEntity(parser, spark).run(isLookUpService);
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new SparkUpdateEntity(parser, spark).run(isLookUpService);
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long organizations = spark.read().load(testDedupGraphBasePath + "/organization").count();
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long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
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long publications = spark.read().load(testDedupGraphBasePath + "/publication").count();
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long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
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System.out.println("publications = " + publications);
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long mergedOrgs = spark
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System.out.println("organizations = " + organizations);
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.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class))
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.where("relClass=='merges'")
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.javaRDD()
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.map(Relation::getTarget)
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.distinct().count();
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long mergedPubs = spark
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.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").as(Encoders.bean(Relation.class))
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.where("relClass=='merges'")
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.javaRDD()
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.map(Relation::getTarget)
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.distinct().count();
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assertEquals(897, publications);
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assertEquals(835, organizations);
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long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization")
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.filter(this::isDeletedByInference).count();
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long deletedPubs = jsc.textFile(testDedupGraphBasePath + "/publication")
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.filter(this::isDeletedByInference).count();
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assertEquals(mergedOrgs, deletedOrgs);
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assertEquals(mergedPubs, deletedPubs);
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//TODO check the size of other entities not deduplicated
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}
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}
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@Test
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@Test
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@ -183,22 +205,13 @@ public class SparkDedupTest {
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new SparkPropagateRelation(parser, spark).run(isLookUpService);
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new SparkPropagateRelation(parser, spark).run(isLookUpService);
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long relations = spark.read().load(testDedupGraphBasePath + "/relation").count();
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long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
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System.out.println("relations = " + relations);
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assertEquals(826, relations);
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}
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}
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@Disabled("must be parametrized to run locally")
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public boolean isDeletedByInference(String s) {
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public void testHashCode() {
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return s.contains("\"deletedbyinference\":true");
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final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f";
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final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46";
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final HashFunction hashFunction = Hashing.murmur3_128();
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System.out.println(s1.hashCode());
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System.out.println(hashFunction.hashString(s1).asLong());
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System.out.println(s2.hashCode());
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System.out.println(hashFunction.hashString(s2).asLong());
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}
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}
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}
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}
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@ -144,7 +144,7 @@
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}
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}
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},
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},
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"model" : [
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"model" : [
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{ "name" : "country", "type" : "String", "path" : "$.organization.metadata.country.classid"},
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{ "name" : "country", "type" : "String", "path" : "$.country.classid"},
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{ "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"},
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{ "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"},
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{ "name" : "legalname", "type" : "String", "path" : "$.legalname.value" },
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{ "name" : "legalname", "type" : "String", "path" : "$.legalname.value" },
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{ "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" },
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{ "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" },
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File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
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@ -0,0 +1,500 @@
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{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|openaire____::007a4870b31056f89b768cf508e1538e", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
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{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::9ea9c0996c87e1dc7fc69f94b5ed0010", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556"}
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{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|openaire____::d0bbea1f5bed5864d1904eb602e608a6", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556"}
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{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|openaire____::c24a458004a31f9687089ea3d249de51", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747"}
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{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::8de0f5a712997aafe0d794a53e51b75a", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|MetisRadboud::f66f1bd369679b5b077dcdf006089556"}
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{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|openaire____::b58bdbe8ae5acead04fc76777d2f8017", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|MetisRadboud::f66f1bd369679b5b077dcdf006089556"}
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{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::7b0e908419508cafb77acfa8ace3af84", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556"}
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{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|openaire____::c978e29d3b2ddf4f0c2b6e60d6613426", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|NARCIS__cris::f66f1bd369679b5b077dcdf006089556"}
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{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|dedup_wf_001::3306689f53b33bac1f1b23a58a0b621b", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556"}
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|
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{"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.7200000000000001"}, "target": "50|test_pubs___::69550235a4bd75fd24dc984b508e721c", "lastupdatetimestamp": 1585327611869, "relType": "resultResult", "source": "50|datacite____::4b128cfa6257d69fd4357501dd2009ff"}
|
||||||
|
{"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "", "classname": "", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.7200000000000001"}, "target": "50|test_pubs___::2e224140e25091c872bd2d97560d4cf0", "lastupdatetimestamp": 1585327520009, "relType": "resultResult", "source": "50|datacite____::4d444c00a5a83437106f588506c29871"}
|
||||||
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Reference in New Issue