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Improvements and refactoring in Dedup #367

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giambattista.bloisi merged 5 commits from dedup_increasenumofblocks into beta 2024-01-11 11:24:07 +01:00
Conversation 0 Commits 5 Files Changed 55 +158 -101
2 changed files with 158 additions and 101 deletions
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255
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
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@ -1,130 +1,187 @@
package eu.dnetlib.dhp.oa.dedup;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.ReduceFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.dedup.model.Identifier;
import eu.dnetlib.dhp.oa.merge.AuthorMerger;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result;
import org.apache.commons.beanutils.BeanUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.ReduceFunction;
import org.apache.spark.sql.*;
import scala.Tuple2;
import scala.Tuple3;
import scala.collection.JavaConversions;
import java.util.*;
import java.util.stream.Stream;
public class DedupRecordFactory {
public static final class DedupRecordReduceState {
public final String dedupId;
protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
public final ArrayList<String> aliases = new ArrayList<>();
private DedupRecordFactory() {
}
public final HashSet<String> acceptanceDate = new HashSet<>();
public static <T extends OafEntity> Dataset<T> createDedupRecord(
final SparkSession spark,
final DataInfo dataInfo,
final String mergeRelsInputPath,
final String entitiesInputPath,
final Class<T> clazz) {
public OafEntity entity;
long ts = System.currentTimeMillis();
public DedupRecordReduceState(String dedupId, String id, OafEntity entity) {
this.dedupId = dedupId;
this.entity = entity;
if (entity == null) {
aliases.add(id);
} else {
if (Result.class.isAssignableFrom(entity.getClass())) {
Result result = (Result) entity;
if (result.getDateofacceptance() != null && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) {
acceptanceDate.add(result.getDateofacceptance().getValue());
}
}
}
}
// <id, json_entity>
Dataset<Row> entities = spark
.read()
.schema(Encoders.bean(clazz).schema())
.json(entitiesInputPath)
.as(Encoders.bean(clazz))
.map(
(MapFunction<T, Tuple2<String, T>>) entity -> {
return new Tuple2<>(entity.getId(), entity);
},
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
.selectExpr("_1 AS id", "_2 AS kryoObject");
public String getDedupId() {
return dedupId;
}
}
private static final int MAX_ACCEPTANCE_DATE = 20;
// <source, target>: source is the dedup_id, target is the id of the mergedIn
Dataset<Row> mergeRels = spark
.read()
.load(mergeRelsInputPath)
.where("relClass == 'merges'")
.selectExpr("source as dedupId", "target as id");
private DedupRecordFactory() {
}
return mergeRels
.join(entities, "id")
.select("dedupId", "kryoObject")
.as(Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)))
.groupByKey((MapFunction<Tuple2<String, T>, String>) Tuple2::_1, Encoders.STRING())
.reduceGroups(
(ReduceFunction<Tuple2<String, T>>) (t1, t2) -> new Tuple2<>(t1._1(),
reduceEntity(t1._1(), t1._2(), t2._2(), clazz)))
.map(
(MapFunction<Tuple2<String, Tuple2<String, T>>, T>) t -> {
T res = t._2()._2();
res.setDataInfo(dataInfo);
res.setLastupdatetimestamp(ts);
return res;
},
Encoders.bean(clazz));
}
public static Dataset<OafEntity> createDedupRecord(
final SparkSession spark,
final DataInfo dataInfo,
final String mergeRelsInputPath,
final String entitiesInputPath,
final Class<OafEntity> clazz) {
public static <T extends OafEntity> T reduceEntity(
String id, T entity, T duplicate, Class<T> clazz) {
final long ts = System.currentTimeMillis();
final Encoder<OafEntity> beanEncoder = Encoders.bean(clazz);
final Encoder<OafEntity> kryoEncoder = Encoders.kryo(clazz);
int compare = new IdentifierComparator()
.compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate));
// <id, json_entity>
Dataset<Row> entities = spark
.read()
.schema(Encoders.bean(clazz).schema())
.json(entitiesInputPath)
.as(beanEncoder)
.map(
(MapFunction<OafEntity, Tuple2<String, OafEntity>>) entity -> {
return new Tuple2<>(entity.getId(), entity);
},
Encoders.tuple(Encoders.STRING(), kryoEncoder))
.selectExpr("_1 AS id", "_2 AS kryoObject");
if (compare > 0) {
T swap = duplicate;
duplicate = entity;
entity = swap;
// <source, target>: source is the dedup_id, target is the id of the mergedIn
Dataset<Row> mergeRels = spark
.read()
.load(mergeRelsInputPath)
.where("relClass == 'merges'")
.selectExpr("source as dedupId", "target as id");
return mergeRels
.join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left")
.select("dedupId", "id", "kryoObject")
.as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder))
.map((MapFunction<Tuple3<String, String, OafEntity>, DedupRecordReduceState>) t -> new DedupRecordReduceState(t._1(), t._2(), t._3()), Encoders.kryo(DedupRecordReduceState.class))
.groupByKey((MapFunction<DedupRecordReduceState, String>) DedupRecordReduceState::getDedupId, Encoders.STRING())
.reduceGroups(
(ReduceFunction<DedupRecordReduceState>) (t1, t2) -> {
if (t1.entity == null) {
t2.aliases.addAll(t1.aliases);
return t2;
}
if (t1.acceptanceDate.size() < MAX_ACCEPTANCE_DATE) {
t1.acceptanceDate.addAll(t2.acceptanceDate);
}
t1.aliases.addAll(t2.aliases);
t1.entity = reduceEntity(t1.entity, t2.entity);
return t1;
}
)
.flatMap
((FlatMapFunction<Tuple2<String, DedupRecordReduceState>, OafEntity>) t -> {
String dedupId = t._1();
DedupRecordReduceState agg = t._2();
if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) {
return Collections.emptyIterator();
}
return Stream.concat(Stream.of(agg.getDedupId()), agg.aliases.stream())
.map(id -> {
try {
OafEntity res = (OafEntity) BeanUtils.cloneBean(agg.entity);
res.setId(id);
res.setDataInfo(dataInfo);
res.setLastupdatetimestamp(ts);
return res;
} catch (Exception e) {
throw new RuntimeException(e);
}
}).iterator();
}, beanEncoder);
}
private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) {
if (duplicate == null) {
return entity;
}
entity.mergeFrom(duplicate);
entity.setId(id);
if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result re = (Result) entity;
Result rd = (Result) duplicate;
int compare = new IdentifierComparator<>()
.compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate));
List<List<Author>> authors = new ArrayList<>();
if (re.getAuthor() != null) {
authors.add(re.getAuthor());
}
if (rd.getAuthor() != null) {
authors.add(rd.getAuthor());
}
if (compare > 0) {
OafEntity swap = duplicate;
duplicate = entity;
entity = swap;
}
re.setAuthor(AuthorMerger.merge(authors));
}
entity.mergeFrom(duplicate);
return entity;
}
if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result re = (Result) entity;
Result rd = (Result) duplicate;
public static <T extends OafEntity> T entityMerger(
String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz)
throws IllegalAccessException, InstantiationException, InvocationTargetException {
T base = entities.next()._2();
List<List<Author>> authors = new ArrayList<>();
if (re.getAuthor() != null) {
authors.add(re.getAuthor());
}
if (rd.getAuthor() != null) {
authors.add(rd.getAuthor());
}
while (entities.hasNext()) {
T duplicate = entities.next()._2();
if (duplicate != null)
base = reduceEntity(id, base, duplicate, clazz);
}
re.setAuthor(AuthorMerger.merge(authors));
}
base.setDataInfo(dataInfo);
base.setLastupdatetimestamp(ts);
return entity;
}
return base;
}
public static <T extends OafEntity> T entityMerger(
String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz) {
T base = entities.next()._2();
while (entities.hasNext()) {
T duplicate = entities.next()._2();
if (duplicate != null)
base = (T) reduceEntity(base, duplicate);
}
base.setId(id);
base.setDataInfo(dataInfo);
base.setLastupdatetimestamp(ts);
return base;
}
}

4
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
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@ -611,7 +611,7 @@ public class SparkDedupTest implements Serializable {
assertEquals(91, pubs.count());
assertEquals(47, sw_deduprecord);
assertEquals(97, ds_deduprecord);
assertEquals(93, orp_deduprecord);
assertEquals(92, orp_deduprecord);
verifyRoot_1(mapper, pubs);
@ -751,7 +751,7 @@ public class SparkDedupTest implements Serializable {
assertEquals(100, datasource);
assertEquals(196, softwares);
assertEquals(389, dataset);
assertEquals(521, otherresearchproduct);
assertEquals(520, otherresearchproduct);
// System.out.println("publications = " + publications);
// System.out.println("organizations = " + organizations);