Merge pull request '[graph dedup] records stability and testing' (#44) from deduptesting into beta

Reviewed-on: #44
This commit is contained in:
Claudio Atzori 2022-12-02 14:43:05 +01:00
commit 41f7f1bbc5
15 changed files with 978 additions and 158 deletions

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@ -1,10 +1,12 @@
package eu.dnetlib.dhp.oa.dedup; package eu.dnetlib.dhp.oa.dedup;
import java.util.Collection; import java.lang.reflect.InvocationTargetException;
import java.util.Iterator; import java.util.*;
import java.util.List; import java.util.stream.Collectors;
import org.apache.commons.beanutils.BeanUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
@ -15,6 +17,7 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists; import com.google.common.collect.Lists;
import eu.dnetlib.dhp.oa.dedup.model.Identifier;
import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.oa.merge.AuthorMerger;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
@ -74,33 +77,42 @@ public class DedupRecordFactory {
public static <T extends OafEntity> T entityMerger( public static <T extends OafEntity> T entityMerger(
String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz) String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz)
throws IllegalAccessException, InstantiationException { throws IllegalAccessException, InstantiationException, InvocationTargetException {
T entity = clazz.newInstance(); final Comparator<Identifier<T>> idComparator = new IdentifierComparator<>();
entity.setDataInfo(dataInfo);
final LinkedList<T> entityList = Lists
.newArrayList(entities)
.stream()
.map(t -> Identifier.newInstance(t._2()))
.sorted(idComparator)
.map(Identifier::getEntity)
.collect(Collectors.toCollection(LinkedList::new));
final T entity = clazz.newInstance();
final T first = entityList.removeFirst();
BeanUtils.copyProperties(entity, first);
final Collection<String> dates = Lists.newArrayList(); final Collection<String> dates = Lists.newArrayList();
final List<List<Author>> authors = Lists.newArrayList(); final List<List<Author>> authors = Lists.newArrayList();
entities entityList
.forEachRemaining( .forEach(
t -> { duplicate -> {
T duplicate = t._2();
entity.mergeFrom(duplicate); entity.mergeFrom(duplicate);
if (ModelSupport.isSubClass(duplicate, Result.class)) { if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result r1 = (Result) duplicate; Result r1 = (Result) duplicate;
if (r1.getAuthor() != null && !r1.getAuthor().isEmpty()) if (r1.getAuthor() != null && StringUtils.isNotBlank(r1.getDateofacceptance().getValue()))
authors.add(r1.getAuthor()); authors.add(r1.getAuthor());
if (r1.getDateofacceptance() != null) if (r1.getDateofacceptance() != null)
dates.add(r1.getDateofacceptance().getValue()); dates.add(r1.getDateofacceptance().getValue());
} }
}); });
// set authors and date // set authors and date
if (ModelSupport.isSubClass(entity, Result.class)) { if (ModelSupport.isSubClass(entity, Result.class)) {
((Result) entity).setDateofacceptance(DatePicker.pick(dates)); // ((Result) entity).setDateofacceptance(DatePicker.pick(dates));
((Result) entity).setAuthor(AuthorMerger.merge(authors)); ((Result) entity).setAuthor(AuthorMerger.merge(authors));
} }

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@ -18,6 +18,10 @@ public class IdGenerator implements Serializable {
if (pids == null || pids.isEmpty()) if (pids == null || pids.isEmpty())
return defaultID; return defaultID;
return generateId(pids);
}
private static <T extends OafEntity> String generateId(List<Identifier<T>> pids) {
Identifier<T> bp = pids Identifier<T> bp = pids
.stream() .stream()
.min(Identifier::compareTo) .min(Identifier::compareTo)

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@ -0,0 +1,81 @@
package eu.dnetlib.dhp.oa.dedup;
import java.util.Comparator;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.oa.dedup.model.Identifier;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.schema.oaf.utils.PidComparator;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
public class IdentifierComparator<T extends OafEntity> implements Comparator<Identifier<T>> {
public static int compareIdentifiers(Identifier left, Identifier right) {
return new IdentifierComparator<>().compare(left, right);
}
@Override
public int compare(Identifier<T> left, Identifier<T> i) {
// priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4)
// alphabetical order of the originalID
Set<String> lKeys = Optional
.ofNullable(left.getCollectedFrom())
.map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
.orElse(Sets.newHashSet());
final Optional<List<KeyValue>> cf = Optional.ofNullable(i.getCollectedFrom());
Set<String> rKeys = cf
.map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
.orElse(Sets.newHashSet());
if (left.getPidType().compareTo(i.getPidType()) == 0) { // same type
if (left.getEntityType() == EntityType.publication) {
if (isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID)
&& !isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID))
return -1;
if (isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID)
&& !isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID))
return 1;
}
if (left.getEntityType() == EntityType.dataset) {
if (isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID)
&& !isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID))
return -1;
if (isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID)
&& !isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID))
return 1;
}
if (left.getDate().compareTo(i.getDate()) == 0) {// same date
// we need to take the alphabetically lower id
return left.getOriginalID().compareTo(i.getOriginalID());
} else
// we need to take the elder date
return left.getDate().compareTo(i.getDate());
} else {
return new PidComparator<>(left.getEntity()).compare(toSP(left.getPidType()), toSP(i.getPidType()));
}
}
public boolean isFromDatasourceID(Set<String> collectedFrom, String dsId) {
return collectedFrom.contains(dsId);
}
private StructuredProperty toSP(PidType pidType) {
return OafMapperUtils.structuredProperty("", pidType.toString(), pidType.toString(), "", "", new DataInfo());
}
}

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@ -11,6 +11,7 @@ import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Sets; import com.google.common.collect.Sets;
import eu.dnetlib.dhp.oa.dedup.DatePicker; import eu.dnetlib.dhp.oa.dedup.DatePicker;
import eu.dnetlib.dhp.oa.dedup.IdentifierComparator;
import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
@ -83,60 +84,12 @@ public class Identifier<T extends OafEntity> implements Serializable, Comparable
return entity.getId(); return entity.getId();
} }
private PidType getPidType() { public PidType getPidType() {
return PidType.tryValueOf(StringUtils.substringBefore(StringUtils.substringAfter(entity.getId(), "|"), "_")); return PidType.tryValueOf(StringUtils.substringBefore(StringUtils.substringAfter(entity.getId(), "|"), "_"));
} }
@Override @Override
public int compareTo(Identifier<T> i) { public int compareTo(Identifier<T> i) {
// priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4) return IdentifierComparator.compareIdentifiers(this, i);
// alphabetical order of the originalID
Set<String> lKeys = Optional
.ofNullable(getCollectedFrom())
.map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
.orElse(Sets.newHashSet());
final Optional<List<KeyValue>> cf = Optional.ofNullable(i.getCollectedFrom());
Set<String> rKeys = cf
.map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
.orElse(Sets.newHashSet());
if (this.getPidType().compareTo(i.getPidType()) == 0) { // same type
if (getEntityType() == EntityType.publication) {
if (isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID)
&& !isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID))
return -1;
if (isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID)
&& !isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID))
return 1;
}
if (getEntityType() == EntityType.dataset) {
if (isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID)
&& !isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID))
return -1;
if (isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID)
&& !isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID))
return 1;
}
if (this.getDate().compareTo(i.getDate()) == 0) {// same date
// we need to take the alphabetically lower id
return this.getOriginalID().compareTo(i.getOriginalID());
} else
// we need to take the elder date
return this.getDate().compareTo(i.getDate());
} else {
return new PidComparator<>(getEntity()).compare(toSP(getPidType()), toSP(i.getPidType()));
}
}
private StructuredProperty toSP(PidType pidType) {
return OafMapperUtils.structuredProperty("", pidType.toString(), pidType.toString(), "", "", new DataInfo());
}
public boolean isFromDatasourceID(Set<String> collectedFrom, String dsId) {
return collectedFrom.contains(dsId);
} }
} }

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@ -7,6 +7,7 @@ import java.io.BufferedReader;
import java.io.FileReader; import java.io.FileReader;
import java.io.IOException; import java.io.IOException;
import java.io.Serializable; import java.io.Serializable;
import java.lang.reflect.InvocationTargetException;
import java.nio.file.Paths; import java.nio.file.Paths;
import java.util.*; import java.util.*;
import java.util.stream.Collectors; import java.util.stream.Collectors;
@ -54,7 +55,7 @@ class EntityMergerTest implements Serializable {
} }
@Test @Test
void softwareMergerTest() throws InstantiationException, IllegalAccessException { void softwareMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
List<Tuple2<String, Software>> softwares = readSample( List<Tuple2<String, Software>> softwares = readSample(
testEntityBasePath + "/software_merge.json", Software.class); testEntityBasePath + "/software_merge.json", Software.class);
@ -69,7 +70,7 @@ class EntityMergerTest implements Serializable {
} }
@Test @Test
void publicationMergerTest() throws InstantiationException, IllegalAccessException { void publicationMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
Publication pub_merged = DedupRecordFactory Publication pub_merged = DedupRecordFactory
.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class); .entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class);
@ -134,7 +135,7 @@ class EntityMergerTest implements Serializable {
} }
@Test @Test
void publicationMergerTest2() throws InstantiationException, IllegalAccessException { void publicationMergerTest2() throws InstantiationException, IllegalAccessException, InvocationTargetException {
Publication pub_merged = DedupRecordFactory Publication pub_merged = DedupRecordFactory
.entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class);
@ -146,7 +147,7 @@ class EntityMergerTest implements Serializable {
} }
@Test @Test
void publicationMergerTest3() throws InstantiationException, IllegalAccessException { void publicationMergerTest3() throws InstantiationException, IllegalAccessException, InvocationTargetException {
Publication pub_merged = DedupRecordFactory Publication pub_merged = DedupRecordFactory
.entityMerger(dedupId, publications3.iterator(), 0, dataInfo, Publication.class); .entityMerger(dedupId, publications3.iterator(), 0, dataInfo, Publication.class);
@ -156,7 +157,8 @@ class EntityMergerTest implements Serializable {
} }
@Test @Test
void publicationMergerTest4() throws InstantiationException, IllegalStateException, IllegalAccessException { void publicationMergerTest4()
throws InstantiationException, IllegalStateException, IllegalAccessException, InvocationTargetException {
Publication pub_merged = DedupRecordFactory Publication pub_merged = DedupRecordFactory
.entityMerger(dedupId, publications4.iterator(), 0, dataInfo, Publication.class); .entityMerger(dedupId, publications4.iterator(), 0, dataInfo, Publication.class);
@ -166,7 +168,8 @@ class EntityMergerTest implements Serializable {
} }
@Test @Test
void publicationMergerTest5() throws InstantiationException, IllegalStateException, IllegalAccessException { void publicationMergerTest5()
throws InstantiationException, IllegalStateException, IllegalAccessException, InvocationTargetException {
System.out System.out
.println( .println(

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@ -4,8 +4,7 @@ package eu.dnetlib.dhp.oa.dedup;
import static java.nio.file.Files.createTempDirectory; import static java.nio.file.Files.createTempDirectory;
import static org.apache.spark.sql.functions.count; import static org.apache.spark.sql.functions.count;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.Mockito.lenient; import static org.mockito.Mockito.lenient;
import java.io.File; import java.io.File;
@ -14,7 +13,11 @@ import java.io.IOException;
import java.io.Serializable; import java.io.Serializable;
import java.net.URISyntaxException; import java.net.URISyntaxException;
import java.nio.file.Paths; import java.nio.file.Paths;
import java.util.HashSet;
import java.util.List; import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -35,10 +38,13 @@ import org.mockito.Mock;
import org.mockito.Mockito; import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
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 eu.dnetlib.pace.util.MapDocumentUtil; import eu.dnetlib.pace.util.MapDocumentUtil;
@ -105,57 +111,27 @@ public class SparkDedupTest implements Serializable {
lenient() lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
.thenReturn( .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"));
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
lenient() lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
.thenReturn( .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"));
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
lenient() lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
.thenReturn( .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"));
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
lenient() lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
.thenReturn( .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"));
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
lenient() lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset"))) .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset")))
.thenReturn( .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json"));
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")));
lenient() lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct"))) .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct")))
.thenReturn( .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json"));
IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")));
} }
@Test @Test
@ -163,11 +139,7 @@ public class SparkDedupTest implements Serializable {
void createSimRelsTest() throws Exception { void createSimRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"));
.toString(
SparkCreateSimRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
parser parser
.parseArgument( .parseArgument(
@ -207,7 +179,7 @@ public class SparkDedupTest implements Serializable {
.count(); .count();
assertEquals(3076, orgs_simrel); assertEquals(3076, orgs_simrel);
assertEquals(7040, pubs_simrel); assertEquals(7046, pubs_simrel);
assertEquals(336, sw_simrel); assertEquals(336, sw_simrel);
assertEquals(442, ds_simrel); assertEquals(442, ds_simrel);
assertEquals(6784, orp_simrel); assertEquals(6784, orp_simrel);
@ -223,11 +195,7 @@ public class SparkDedupTest implements Serializable {
void whitelistSimRelsTest() throws Exception { void whitelistSimRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json"));
.toString(
SparkWhitelistSimRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
parser parser
.parseArgument( .parseArgument(
@ -264,7 +232,7 @@ public class SparkDedupTest implements Serializable {
// entities simrels supposed to be equal to the number of previous step (no rels in whitelist) // entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
assertEquals(3076, orgs_simrel); assertEquals(3076, orgs_simrel);
assertEquals(7040, pubs_simrel); assertEquals(7046, pubs_simrel);
assertEquals(442, ds_simrel); assertEquals(442, ds_simrel);
assertEquals(6784, orp_simrel); assertEquals(6784, orp_simrel);
// System.out.println("orgs_simrel = " + orgs_simrel); // System.out.println("orgs_simrel = " + orgs_simrel);
@ -306,11 +274,7 @@ public class SparkDedupTest implements Serializable {
void cutMergeRelsTest() throws Exception { void cutMergeRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"));
.toString(
SparkCreateMergeRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
parser parser
.parseArgument( .parseArgument(
@ -402,11 +366,7 @@ public class SparkDedupTest implements Serializable {
void createMergeRelsTest() throws Exception { void createMergeRelsTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"));
.toString(
SparkCreateMergeRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
parser parser
.parseArgument( .parseArgument(
@ -427,10 +387,10 @@ public class SparkDedupTest implements Serializable {
.read() .read()
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
.count(); .count();
long pubs_mergerel = spark final Dataset<Relation> pubs = spark
.read() .read()
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
.count(); .as(Encoders.bean(Relation.class));
long sw_mergerel = spark long sw_mergerel = spark
.read() .read()
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
@ -445,8 +405,35 @@ public class SparkDedupTest implements Serializable {
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
.count(); .count();
final List<Relation> merges = pubs
.filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
.collectAsList();
assertEquals(3, merges.size());
Set<String> dups = Sets
.newHashSet(
"50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73",
"50|doi_________::d5021b53204e4fdeab6ff5d5bc468032",
"50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c");
merges.forEach(r -> {
assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
assertEquals(ModelConstants.DEDUP, r.getSubRelType());
assertEquals(ModelConstants.MERGES, r.getRelClass());
assertTrue(dups.contains(r.getTarget()));
});
final List<Relation> mergedIn = pubs
.filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
.collectAsList();
assertEquals(3, mergedIn.size());
mergedIn.forEach(r -> {
assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
assertEquals(ModelConstants.DEDUP, r.getSubRelType());
assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass());
assertTrue(dups.contains(r.getSource()));
});
assertEquals(1268, orgs_mergerel); assertEquals(1268, orgs_mergerel);
assertEquals(1444, pubs_mergerel); assertEquals(1450, pubs.count());
assertEquals(286, sw_mergerel); assertEquals(286, sw_mergerel);
assertEquals(472, ds_mergerel); assertEquals(472, ds_mergerel);
assertEquals(738, orp_mergerel); assertEquals(738, orp_mergerel);
@ -463,11 +450,7 @@ public class SparkDedupTest implements Serializable {
void createDedupRecordTest() throws Exception { void createDedupRecordTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"));
.toString(
SparkCreateDedupRecord.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
parser parser
.parseArgument( .parseArgument(
new String[] { new String[] {
@ -483,12 +466,18 @@ public class SparkDedupTest implements Serializable {
new SparkCreateDedupRecord(parser, spark).run(isLookUpService); new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
final ObjectMapper mapper = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
final Dataset<Publication> pubs = spark
.read()
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord")
.map(
(MapFunction<String, Publication>) value -> mapper.readValue(value, Publication.class),
Encoders.bean(Publication.class));
long orgs_deduprecord = jsc long orgs_deduprecord = jsc
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord") .textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord")
.count(); .count();
long pubs_deduprecord = jsc
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord")
.count();
long sw_deduprecord = jsc long sw_deduprecord = jsc
.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord") .textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
.count(); .count();
@ -499,11 +488,13 @@ public class SparkDedupTest implements Serializable {
.count(); .count();
assertEquals(86, orgs_deduprecord); assertEquals(86, orgs_deduprecord);
assertEquals(67, pubs_deduprecord); assertEquals(68, pubs.count());
assertEquals(49, sw_deduprecord); assertEquals(49, sw_deduprecord);
assertEquals(97, ds_deduprecord); assertEquals(97, ds_deduprecord);
assertEquals(92, orp_deduprecord); assertEquals(92, orp_deduprecord);
verifyRoot_1(mapper, pubs);
// System.out.println("orgs_deduprecord = " + orgs_deduprecord); // System.out.println("orgs_deduprecord = " + orgs_deduprecord);
// System.out.println("pubs_deduprecord = " + pubs_deduprecord); // System.out.println("pubs_deduprecord = " + pubs_deduprecord);
// System.out.println("sw_deduprecord = " + sw_deduprecord); // System.out.println("sw_deduprecord = " + sw_deduprecord);
@ -511,16 +502,63 @@ public class SparkDedupTest implements Serializable {
// System.out.println("orp_deduprecord = " + orp_deduprecord); // System.out.println("orp_deduprecord = " + orp_deduprecord);
} }
private static void verifyRoot_1(ObjectMapper mapper, Dataset<Publication> pubs) {
Publication root = pubs
.filter("id = '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
.first();
assertNotNull(root);
final Dataset<String> publication = spark
.read()
.textFile(DedupUtility.createEntityPath(testGraphBasePath, "publication"));
Publication crossref_duplicate = publication
.map(
(MapFunction<String, Publication>) value -> mapper.readValue(value, Publication.class),
Encoders.bean(Publication.class))
.filter("id = '50|doi_________::d5021b53204e4fdeab6ff5d5bc468032'")
.collectAsList()
.get(0);
assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName());
assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted());
assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
Set<String> rootPids = root
.getPid()
.stream()
.map(StructuredProperty::getValue)
.collect(Collectors.toCollection(HashSet::new));
Set<String> dupPids = crossref_duplicate
.getPid()
.stream()
.map(StructuredProperty::getValue)
.collect(Collectors.toCollection(HashSet::new));
assertFalse(Sets.intersection(rootPids, dupPids).isEmpty());
assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716"));
Optional<Instance> instance_cr = root
.getInstance()
.stream()
.filter(i -> i.getCollectedfrom().getValue().equals("Crossref"))
.findFirst();
assertTrue(instance_cr.isPresent());
assertEquals("OPEN", instance_cr.get().getAccessright().getClassid());
assertEquals("Open Access", instance_cr.get().getAccessright().getClassname());
assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute());
assertEquals(
"IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue());
assertEquals("0001", instance_cr.get().getInstancetype().getClassid());
assertEquals("Article", instance_cr.get().getInstancetype().getClassname());
}
@Test @Test
@Order(6) @Order(6)
void updateEntityTest() throws Exception { void updateEntityTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"));
.toString(
SparkUpdateEntity.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
parser parser
.parseArgument( .parseArgument(
new String[] { new String[] {
@ -587,7 +625,7 @@ public class SparkDedupTest implements Serializable {
.distinct() .distinct()
.count(); .count();
assertEquals(898, publications); assertEquals(902, publications);
assertEquals(839, organizations); assertEquals(839, organizations);
assertEquals(100, projects); assertEquals(100, projects);
assertEquals(100, datasource); assertEquals(100, datasource);
@ -640,11 +678,7 @@ public class SparkDedupTest implements Serializable {
void propagateRelationTest() throws Exception { void propagateRelationTest() throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser( ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"));
.toString(
SparkPropagateRelation.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
parser parser
.parseArgument( .parseArgument(
new String[] { new String[] {
@ -714,4 +748,12 @@ public class SparkDedupTest implements Serializable {
public boolean isDeletedByInference(String s) { public boolean isDeletedByInference(String s) {
return s.contains("\"deletedbyinference\":true"); return s.contains("\"deletedbyinference\":true");
} }
private static String classPathResourceAsString(String path) throws IOException {
return IOUtils
.toString(
SparkDedupTest.class
.getResourceAsStream(path));
}
} }

View File

@ -143,7 +143,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
.count(); .count();
assertEquals(288, orgs_simrel); assertEquals(290, orgs_simrel);
} }
@Test @Test
@ -172,7 +172,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
.count(); .count();
assertEquals(324, orgs_simrel); assertEquals(326, orgs_simrel);
} }
@Test @Test

View File

@ -0,0 +1,403 @@
package eu.dnetlib.dhp.oa.dedup;
import static java.nio.file.Files.createTempDirectory;
import static org.apache.spark.sql.functions.count;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.lenient;
import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.net.URISyntaxException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
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 com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class SparkPublicationRootsTest implements Serializable {
@Mock(serializable = true)
ISLookUpService isLookUpService;
private static SparkSession spark;
private static String workingPath;
private static String graphInputPath;
private static String graphOutputPath;
private static final String testActionSetId = "test-orchestrator";
private static Path testBaseTmpPath;
private static final ObjectMapper MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@BeforeAll
public static void init() throws IOException, URISyntaxException {
testBaseTmpPath = createTempDirectory(SparkPublicationRootsTest.class.getSimpleName() + "-");
final File entitiesSources = Paths
.get(SparkPublicationRootsTest.class.getResource("/eu/dnetlib/dhp/dedup/root").toURI())
.toFile();
FileUtils
.copyDirectory(
entitiesSources,
testBaseTmpPath.resolve("input").toFile());
workingPath = testBaseTmpPath.resolve("workingPath").toString();
graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString();
graphOutputPath = testBaseTmpPath.resolve("output").toString();
FileUtils.deleteDirectory(new File(workingPath));
FileUtils.deleteDirectory(new File(graphOutputPath));
final SparkConf conf = new SparkConf();
conf.set("spark.sql.shuffle.partitions", "10");
spark = SparkSession
.builder()
.appName(SparkPublicationRootsTest.class.getSimpleName())
.master("local[*]")
.config(conf)
.getOrCreate();
}
@BeforeEach
public void setUp() throws IOException, ISLookUpException {
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml"));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"));
}
@AfterAll
public static void tearDown() throws IOException {
FileUtils.deleteDirectory(testBaseTmpPath.toFile());
spark.close();
}
@Test
@Order(1)
void createSimRelsTest() throws Exception {
new SparkCreateSimRels(args(
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json",
new String[] {
"--graphBasePath", graphInputPath,
"--actionSetId", testActionSetId,
"--isLookUpUrl", "lookupurl",
"--workingPath", workingPath,
"--numPartitions", "5"
}), spark)
.run(isLookUpService);
long pubs_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(workingPath, testActionSetId, "publication"))
.count();
assertEquals(74, pubs_simrel);
}
@Test
@Order(2)
void cutMergeRelsTest() throws Exception {
new SparkCreateMergeRels(args(
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json",
new String[] {
"--graphBasePath", graphInputPath,
"--actionSetId", testActionSetId,
"--isLookUpUrl", "lookupurl",
"--workingPath", workingPath,
"--cutConnectedComponent", "3"
}), spark)
.run(isLookUpService);
long pubs_mergerel = spark
.read()
.load(workingPath + "/" + testActionSetId + "/publication_mergerel")
.as(Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
.groupBy("source")
.agg(count("target").alias("cnt"))
.select("source", "cnt")
.where("cnt > 3")
.count();
assertEquals(0, pubs_mergerel);
FileUtils.deleteDirectory(new File(workingPath + "/" + testActionSetId + "/publication_mergerel"));
}
@Test
@Order(3)
void createMergeRelsTest() throws Exception {
new SparkCreateMergeRels(args(
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json",
new String[] {
"--graphBasePath", graphInputPath,
"--actionSetId", testActionSetId,
"--isLookUpUrl", "lookupurl",
"--workingPath", workingPath
}), spark)
.run(isLookUpService);
final Dataset<Relation> merges = spark
.read()
.load(workingPath + "/" + testActionSetId + "/publication_mergerel")
.as(Encoders.bean(Relation.class));
final List<Relation> mergeList = merges
.filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
.collectAsList();
assertEquals(3, mergeList.size());
Set<String> dups = Sets
.newHashSet(
"50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73",
"50|doi_________::d5021b53204e4fdeab6ff5d5bc468032",
"50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c");
mergeList.forEach(r -> {
assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
assertEquals(ModelConstants.DEDUP, r.getSubRelType());
assertEquals(ModelConstants.MERGES, r.getRelClass());
assertTrue(dups.contains(r.getTarget()));
});
final List<Relation> mergedIn = merges
.filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
.collectAsList();
assertEquals(3, mergedIn.size());
mergedIn.forEach(r -> {
assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
assertEquals(ModelConstants.DEDUP, r.getSubRelType());
assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass());
assertTrue(dups.contains(r.getSource()));
});
assertEquals(32, merges.count());
}
@Test
@Order(4)
void createDedupRecordTest() throws Exception {
new SparkCreateDedupRecord(args(
"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json",
new String[] {
"--graphBasePath", graphInputPath,
"--actionSetId", testActionSetId,
"--isLookUpUrl", "lookupurl",
"--workingPath", workingPath
}), spark)
.run(isLookUpService);
final Dataset<Publication> roots = spark
.read()
.textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord")
.map(asEntity(Publication.class), Encoders.bean(Publication.class));
assertEquals(3, roots.count());
final Dataset<Publication> pubs = spark
.read()
.textFile(DedupUtility.createEntityPath(graphInputPath, "publication"))
.map(asEntity(Publication.class), Encoders.bean(Publication.class));
verifyRoot_case_1(roots, pubs);
verifyRoot_case_2(roots, pubs);
verifyRoot_case_3(roots, pubs);
}
private static void verifyRoot_case_1(Dataset<Publication> roots, Dataset<Publication> pubs) {
Publication root = roots
.filter("id = '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'")
.first();
assertNotNull(root);
Publication crossref_duplicate = pubs
.filter("id = '50|doi_________::d5021b53204e4fdeab6ff5d5bc468032'")
.collectAsList()
.get(0);
assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName());
assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted());
assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
Set<String> rootPids = root
.getPid()
.stream()
.map(StructuredProperty::getValue)
.collect(Collectors.toCollection(HashSet::new));
Set<String> dupPids = crossref_duplicate
.getPid()
.stream()
.map(StructuredProperty::getValue)
.collect(Collectors.toCollection(HashSet::new));
assertFalse(Sets.intersection(rootPids, dupPids).isEmpty());
assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716"));
Optional<Instance> instance_cr = root
.getInstance()
.stream()
.filter(i -> i.getCollectedfrom().getValue().equals("Crossref"))
.findFirst();
assertTrue(instance_cr.isPresent());
assertEquals("OPEN", instance_cr.get().getAccessright().getClassid());
assertEquals("Open Access", instance_cr.get().getAccessright().getClassname());
assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute());
assertEquals(
"IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue());
assertEquals("0001", instance_cr.get().getInstancetype().getClassid());
assertEquals("Article", instance_cr.get().getInstancetype().getClassname());
}
private void verifyRoot_case_2(Dataset<Publication> roots, Dataset<Publication> pubs) {
Publication root = roots
.filter("id = '50|doi_dedup___::18aff3b55fb6876466a5d4bd82434885'")
.first();
assertNotNull(root);
Publication crossref_duplicate = pubs
.filter("id = '50|doi_________::18aff3b55fb6876466a5d4bd82434885'")
.first();
// System.err.println(new ObjectMapper().writeValueAsString(root));
assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName());
assertEquals(crossref_duplicate.getJournal().getIssnOnline(), root.getJournal().getIssnOnline());
assertEquals(crossref_duplicate.getJournal().getVol(), root.getJournal().getVol());
assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
Set<String> dups_cf = pubs
.collectAsList()
.stream()
.flatMap(p -> p.getCollectedfrom().stream())
.map(KeyValue::getValue)
.collect(Collectors.toCollection(HashSet::new));
Set<String> root_cf = root
.getCollectedfrom()
.stream()
.map(KeyValue::getValue)
.collect(Collectors.toCollection(HashSet::new));
assertTrue(Sets.difference(root_cf, dups_cf).isEmpty());
}
private void verifyRoot_case_3(Dataset<Publication> roots, Dataset<Publication> pubs) {
Publication root = roots
.filter("id = '50|dedup_wf_001::31ca734cc22181b704c4aa8fd050062a'")
.first();
assertNotNull(root);
Publication pivot_duplicate = pubs
.filter("id = '50|od_______166::31ca734cc22181b704c4aa8fd050062a'")
.first();
assertEquals(pivot_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
Set<String> dups_cf = pubs
.collectAsList()
.stream()
.flatMap(p -> p.getCollectedfrom().stream())
.map(KeyValue::getValue)
.collect(Collectors.toCollection(HashSet::new));
Set<String> root_cf = root
.getCollectedfrom()
.stream()
.map(KeyValue::getValue)
.collect(Collectors.toCollection(HashSet::new));
assertTrue(Sets.difference(root_cf, dups_cf).isEmpty());
}
@Test
@Order(6)
void updateEntityTest() throws Exception {
new SparkUpdateEntity(args(
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json",
new String[] {
"--graphBasePath", graphInputPath,
"--workingPath", workingPath,
"--dedupGraphPath", graphOutputPath
}), spark)
.run(isLookUpService);
long publications = spark.read().textFile(graphOutputPath + "/publication").count();
long mergedPubs = spark
.read()
.load(workingPath + "/" + testActionSetId + "/publication_mergerel")
.as(Encoders.bean(Relation.class))
.where("relClass=='merges'")
.map((MapFunction<Relation, String>) Relation::getTarget, Encoders.STRING())
.distinct()
.count();
assertEquals(19, publications); // 16 originals + 3 roots
long deletedPubs = spark
.read()
.textFile(graphOutputPath + "/publication")
.map(asEntity(Publication.class), Encoders.bean(Publication.class))
.filter("datainfo.deletedbyinference == true")
.map((MapFunction<Publication, String>) OafEntity::getId, Encoders.STRING())
.distinct()
.count();
assertEquals(mergedPubs, deletedPubs);
}
private static String classPathResourceAsString(String path) throws IOException {
return IOUtils
.toString(
SparkPublicationRootsTest.class
.getResourceAsStream(path));
}
private static <T extends OafEntity> MapFunction<String, T> asEntity(Class<T> clazz) {
return value -> MAPPER.readValue(value, clazz);
}
private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException {
ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs));
parser.parseArgument(args);
return parser;
}
}

View File

@ -0,0 +1,251 @@
package eu.dnetlib.dhp.oa.dedup;
import static java.nio.file.Files.createTempDirectory;
import static org.apache.spark.sql.functions.count;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.lenient;
import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.net.URISyntaxException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
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 com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class SparkPublicationRootsTest2 implements Serializable {
@Mock(serializable = true)
ISLookUpService isLookUpService;
private static SparkSession spark;
private static String workingPath;
private static String graphInputPath;
private static String graphOutputPath;
private static final String testActionSetId = "test-orchestrator";
private static Path testBaseTmpPath;
private static final ObjectMapper MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@BeforeAll
public static void init() throws IOException, URISyntaxException {
testBaseTmpPath = createTempDirectory(SparkPublicationRootsTest2.class.getSimpleName() + "-");
final File entitiesSources = Paths
.get(SparkPublicationRootsTest2.class.getResource("/eu/dnetlib/dhp/dedup/root").toURI())
.toFile();
FileUtils
.copyDirectory(
entitiesSources,
testBaseTmpPath.resolve("input").toFile());
FileUtils
.copyFileToDirectory(
Paths
.get(
SparkPublicationRootsTest2.class
.getResource(
"/eu/dnetlib/dhp/dedup/root/alterations/publication/publication_1.gz")
.toURI())
.toFile(),
testBaseTmpPath.resolve("input").resolve("entities").resolve("publication").toFile());
workingPath = testBaseTmpPath.resolve("workingPath").toString();
graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString();
graphOutputPath = testBaseTmpPath.resolve("output").toString();
final SparkConf conf = new SparkConf();
conf.set("spark.sql.shuffle.partitions", "10");
spark = SparkSession
.builder()
.appName(SparkPublicationRootsTest2.class.getSimpleName())
.master("local[*]")
.config(conf)
.getOrCreate();
}
@BeforeEach
public void setUp() throws IOException, ISLookUpException {
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml"));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
.thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"));
}
@AfterAll
public static void tearDown() throws IOException {
FileUtils.deleteDirectory(testBaseTmpPath.toFile());
}
@Test
@Order(7)
void dedupAlteredDatasetTest() throws Exception {
new SparkCreateSimRels(args(
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json",
new String[] {
"--graphBasePath", graphInputPath,
"--actionSetId", testActionSetId,
"--isLookUpUrl", "lookupurl",
"--workingPath", workingPath,
"--numPartitions", "5"
}), spark)
.run(isLookUpService);
new SparkCreateMergeRels(args(
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json",
new String[] {
"--graphBasePath", graphInputPath,
"--actionSetId", testActionSetId,
"--isLookUpUrl", "lookupurl",
"--workingPath", workingPath
}), spark)
.run(isLookUpService);
final Dataset<Relation> merges = spark
.read()
.load(workingPath + "/" + testActionSetId + "/publication_mergerel")
.as(Encoders.bean(Relation.class));
assertEquals(
3, merges
.filter("relclass == 'isMergedIn'")
.map((MapFunction<Relation, String>) Relation::getTarget, Encoders.STRING())
.distinct()
.count());
assertEquals(
4, merges
.filter("source == '50|doi_dedup___::b3aec7985136e36827176aaa1dd5082d'")
.count());
new SparkCreateDedupRecord(args(
"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json",
new String[] {
"--graphBasePath", graphInputPath,
"--actionSetId", testActionSetId,
"--isLookUpUrl", "lookupurl",
"--workingPath", workingPath
}), spark)
.run(isLookUpService);
final Dataset<Publication> roots = spark
.read()
.textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord")
.map(asEntity(Publication.class), Encoders.bean(Publication.class));
assertEquals(3, roots.count());
final Dataset<Publication> pubs = spark
.read()
.textFile(DedupUtility.createEntityPath(graphInputPath, "publication"))
.map(asEntity(Publication.class), Encoders.bean(Publication.class));
Publication root = roots
.filter("id = '50|doi_dedup___::b3aec7985136e36827176aaa1dd5082d'")
.first();
assertNotNull(root);
Publication crossref_duplicate = pubs
.filter("id = '50|doi_________::b3aec7985136e36827176aaa1dd5082d'")
.collectAsList()
.get(0);
assertEquals(crossref_duplicate.getDateofacceptance().getValue(), root.getDateofacceptance().getValue());
assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName());
assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted());
assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue());
Set<String> rootPids = root
.getPid()
.stream()
.map(StructuredProperty::getValue)
.collect(Collectors.toCollection(HashSet::new));
Set<String> dupPids = crossref_duplicate
.getPid()
.stream()
.map(StructuredProperty::getValue)
.collect(Collectors.toCollection(HashSet::new));
assertFalse(Sets.intersection(rootPids, dupPids).isEmpty());
assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716"));
assertTrue(rootPids.contains("10.1109/jstqe.2023.9999999"));
Optional<Instance> instance_cr = root
.getInstance()
.stream()
.filter(i -> i.getCollectedfrom().getValue().equals("Crossref"))
.findFirst();
assertTrue(instance_cr.isPresent());
assertEquals("OPEN", instance_cr.get().getAccessright().getClassid());
assertEquals("Open Access", instance_cr.get().getAccessright().getClassname());
assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute());
assertEquals(
"IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue());
assertEquals("0001", instance_cr.get().getInstancetype().getClassid());
assertEquals("Article", instance_cr.get().getInstancetype().getClassname());
}
private static String classPathResourceAsString(String path) throws IOException {
return IOUtils
.toString(
SparkPublicationRootsTest2.class
.getResourceAsStream(path));
}
private static <T extends OafEntity> MapFunction<String, T> asEntity(Class<T> clazz) {
return value -> MAPPER.readValue(value, clazz);
}
private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException {
ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs));
parser.parseArgument(args);
return parser;
}
}

View File

@ -168,11 +168,11 @@ public class SparkStatsTest implements Serializable {
.textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_blockstats") .textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_blockstats")
.count(); .count();
assertEquals(477, orgs_blocks); assertEquals(480, orgs_blocks);
assertEquals(295, pubs_blocks); assertEquals(295, pubs_blocks);
assertEquals(122, sw_blocks); assertEquals(122, sw_blocks);
assertEquals(191, ds_blocks); assertEquals(191, ds_blocks);
assertEquals(171, orp_blocks); assertEquals(178, orp_blocks);
} }
@AfterAll @AfterAll

View File

@ -0,0 +1,24 @@
<RESOURCE_PROFILE>
<HEADER>
<RESOURCE_IDENTIFIER value=""/>
<RESOURCE_TYPE value="DedupOrchestrationDSResourceType"/>
<RESOURCE_KIND value="DedupOrchestrationDSResources"/>
<RESOURCE_URI value=""/>
<DATE_OF_CREATION value="2001-12-31T12:00:00"/>
</HEADER>
<BODY>
<CONFIGURATION enabled="true">
<DEDUPLICATION>
<ENTITY code="20" label="Organization" name="organization"/>
<ACTION_SET id="test-orchestrator"/>
<SCAN_SEQUENCE>
<SCAN id="publication"/>
</SCAN_SEQUENCE>
</DEDUPLICATION>
</CONFIGURATION>
<STATUS>
<LAST_UPDATE value="2001-12-31T12:00:00"/>
</STATUS>
<SECURITY_PARAMETERS>SECURITY_PARAMETERS</SECURITY_PARAMETERS>
</BODY>
</RESOURCE_PROFILE>

View File

@ -0,0 +1,47 @@
# Root logger option
log4j.rootLogger=DEBUG, stdout
# Direct log messages to stdout
log4j.appender.stdout=org.apache.log4j.ConsoleAppender
log4j.appender.stdout.Target=System.out
log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
# Change this to set Spark log level
log4j.logger.org.apache.spark=ERROR
log4j.rootCategory=WARN
# Silence akka remoting
log4j.logger.Remoting=WARN
# Ignore messages below warning level from Jetty, because it's a bit verbose
log4j.logger.org.eclipse.jetty=WARN
log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitterFactory=WARN
log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter=WARN
#log4j.logger.org.apache.parquet.hadoop.ParquetOutputFormat=WARN
#log4j.logger.org.apache.parquet.hadoop.InternalParquetRecordWriter=WARN
log4j.logger.org.apache.hadoop.io.compress.CodecPool=WARN
#log4j.logger.org.apache.hadoop.io.compress=WARN
#log4j.logger.org.apache.parquet.hadoop.codec.CodecConfig=WARN
log4j.logger.parquet.hadoop.ColumnChunkPageWriteStore=ERROR
log4j.logger.com.jayway.jsonpath.internal.path.CompiledPath=WARN
log4j.logger.org.apache.parquet.hadoop.ParquetRecordReader=ERROR
log4j.logger.parquet.hadoop=WARN
log4j.logger.org.eclipse.jetty.server.handler.ContextHandlerCollection=WARN
log4j.logger.org.spark_project.jetty.util.component.ContainerLifeCycle=WARN
log4j.logger.org.apache.hadoop.mapred.FileInputFormat=WARN
log4j.logger.org.spark_project.jetty.servlet.ServletHandler=WARN
log4j.logger.org.apache.commons.beanutils.converters.BooleanConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.StringConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.LongConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.ArrayConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.FloatConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.IntegerConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.DoubleConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.CharacterConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.ByteConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.BigIntegerConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.BigDecimalConverter=WARN
log4j.logger.org.apache.commons.beanutils.converters.ShortConverter=WARN
log4j.logger.org.apache.commons.beanutils.BeanUtils=WARN