further implementation of tests for the deduplication of each entity. publication dump added, empty entity files created

This commit is contained in:
miconis 2020-04-08 18:02:30 +02:00
parent 56fbe689f0
commit 0be2e72be5
11 changed files with 2144 additions and 4098 deletions

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@ -20,7 +20,6 @@ public class MergeAuthorTest {
public void setUp() throws Exception { public void setUp() throws Exception {
final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/json/authors_merge.json")); final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/dedup/json/authors_merge.json"));
publicationsToMerge = Arrays.asList(json.split("\n")).stream().map(s-> { publicationsToMerge = Arrays.asList(json.split("\n")).stream().map(s-> {
try { try {
return mapper.readValue(s, Publication.class); return mapper.readValue(s, Publication.class);

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@ -1,13 +1,14 @@
package eu.dnetlib.dhp.oa.dedup; package eu.dnetlib.dhp.oa.dedup;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; 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.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*; import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
@ -17,20 +18,22 @@ import org.mockito.junit.jupiter.MockitoExtension;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.io.Serializable;
import java.net.URISyntaxException; import java.net.URISyntaxException;
import java.nio.file.Paths; import java.nio.file.Paths;
import static org.mockito.Mockito.when;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.lenient;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
@TestMethodOrder(MethodOrderer.OrderAnnotation.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class SparkDedupTest { public class SparkDedupTest implements Serializable {
@Mock @Mock(serializable = true)
ISLookUpService isLookUpService; ISLookUpService isLookUpService;
private SparkSession spark; private static SparkSession spark;
private static JavaSparkContext jsc;
private static String testGraphBasePath; private static String testGraphBasePath;
private final static String testOutputBasePath = "/tmp/test_dedup_workflow"; private final static String testOutputBasePath = "/tmp/test_dedup_workflow";
@ -43,10 +46,6 @@ public class SparkDedupTest {
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();
FileUtils.deleteDirectory(new File(testOutputBasePath)); FileUtils.deleteDirectory(new File(testOutputBasePath));
}
@BeforeEach
private void setUp() throws IOException, ISLookUpException {
spark = SparkSession spark = SparkSession
.builder() .builder()
@ -55,13 +54,20 @@ public class SparkDedupTest {
.config(new SparkConf()) .config(new SparkConf())
.getOrCreate(); .getOrCreate();
when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) jsc = new JavaSparkContext(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"))); .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
} }
@ -85,11 +91,8 @@ public class SparkDedupTest {
long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_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 pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count();
System.out.println("pubs_simrel = " + pubs_simrel); assertEquals(3288, orgs_simrel);
System.out.println("orgs_simrel = " + orgs_simrel); assertEquals(7260, pubs_simrel);
// assertEquals(918, orgs_simrel);
// assertEquals(0, pubs_simrel);
} }
@Test @Test
@ -111,16 +114,14 @@ public class SparkDedupTest {
long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_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 pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count();
System.out.println("pubs_mergerel = " + pubs_mergerel); assertEquals(1244, orgs_mergerel);
System.out.println("orgs_mergerel = " + orgs_mergerel); assertEquals(1460, pubs_mergerel);
// assertEquals(458, orgs_mergerel);
// assertEquals(0, pubs_mergerel);
} }
@Test @Test
@Order(3) @Order(3)
public void dedupRecordTest() throws Exception { public void createDedupRecordTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString( IOUtils.toString(
@ -134,13 +135,11 @@ public class SparkDedupTest {
new SparkCreateDedupRecord(parser, spark).run(isLookUpService); new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
long orgs_deduprecord = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count(); long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count();
long pubs_deduprecord = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count(); long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count();
System.out.println("pubs_deduprecord = " + pubs_deduprecord); assertEquals(82, orgs_deduprecord);
System.out.println("pubs_deduprecord = " + orgs_deduprecord); assertEquals(66, pubs_deduprecord);
// assertEquals(458, orgs_deduprecord);
// assertEquals(0, pubs_deduprecord);
} }
@Test @Test
@ -159,12 +158,35 @@ public class SparkDedupTest {
new SparkUpdateEntity(parser, spark).run(isLookUpService); new SparkUpdateEntity(parser, spark).run(isLookUpService);
long organizations = spark.read().load(testDedupGraphBasePath + "/organization").count(); long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
long publications = spark.read().load(testDedupGraphBasePath + "/publication").count(); long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
System.out.println("publications = " + publications); long mergedOrgs = spark
System.out.println("organizations = " + organizations); .read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class))
.where("relClass=='merges'")
.javaRDD()
.map(Relation::getTarget)
.distinct().count();
long mergedPubs = spark
.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").as(Encoders.bean(Relation.class))
.where("relClass=='merges'")
.javaRDD()
.map(Relation::getTarget)
.distinct().count();
assertEquals(897, publications);
assertEquals(835, organizations);
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);
//TODO check the size of other entities not deduplicated
} }
@Test @Test
@ -183,22 +205,13 @@ public class SparkDedupTest {
new SparkPropagateRelation(parser, spark).run(isLookUpService); new SparkPropagateRelation(parser, spark).run(isLookUpService);
long relations = spark.read().load(testDedupGraphBasePath + "/relation").count(); long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
System.out.println("relations = " + relations); assertEquals(826, relations);
} }
@Disabled("must be parametrized to run locally") public boolean isDeletedByInference(String s) {
public void testHashCode() { return s.contains("\"deletedbyinference\":true");
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());
} }
} }

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@ -144,7 +144,7 @@
} }
}, },
"model" : [ "model" : [
{ "name" : "country", "type" : "String", "path" : "$.organization.metadata.country.classid"}, { "name" : "country", "type" : "String", "path" : "$.country.classid"},
{ "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"}, { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"},
{ "name" : "legalname", "type" : "String", "path" : "$.legalname.value" }, { "name" : "legalname", "type" : "String", "path" : "$.legalname.value" },
{ "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" }, { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" },

File diff suppressed because one or more lines are too long

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@ -0,0 +1,500 @@
{"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"}
{"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"}
{"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"}
{"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"}
{"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"}
{"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"}
{"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"}
{"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"}
{"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"}
{"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____::fc7459b8fed8c0d47947fe04275251c0", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|OpenstarTs__::f66f1bd369679b5b077dcdf006089556"}
{"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____::89bab7c5a227fc27b2b9cadf475a6b71", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|UnityFVG____::f66f1bd369679b5b077dcdf006089556"}
{"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::47ad6f6b1a95349318679227b28f0c82", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556"}
{"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____::735915884eb439d42953372eaf934782", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|VTTRsInSsCrs::f66f1bd369679b5b077dcdf006089556"}
{"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::33ec6128fcbe39e44e4cae712ae19e43", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|WarsawUniWUT::f66f1bd369679b5b077dcdf006089556"}
{"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____::c004fe42ad769bb2afccc59ea8cd4f77", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|WarsawUniWUT::f66f1bd369679b5b077dcdf006089556"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "user:insert", "classname": "user:insert", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|openaire____::5b6b1502c8296b0c1af0e61d0d3ba915", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|crossref____::b72caa821c05e39fc6849f439171478d"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::34d4c900fb41dbf77b727356d4dda3d3", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00017183dc4c858fb77541985323a4ef"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::b29ae16abb2343c6ffc152666b24ea95", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::000372ccd6d25b515cb975adc84c26b8"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::621c930e0986a1ecd4d88eaa3532579e", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::00041da13243fed6363ec8f6f4bbcb36"}
{"subRelType": "provision", "relClass": "provides", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "target": "20|doajarticles::621c930e0986a1ecd4d88eaa3532579e", "lastupdatetimestamp": 0, "relType": "datasourceOrganization", "source": "10|doajarticles::0009e71a03314001d4b77a9b175487ce"}
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