From 6fd25cf549e3892d3d1f114848367ea00dd84399 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 23 Jan 2024 08:47:12 +0100 Subject: [PATCH] code formatting --- .../eu/dnetlib/dhp/oozie/RunSQLSparkJob.java | 18 +- .../dhp/oa/dedup/DedupRecordFactory.java | 284 +++++++++--------- .../dhp/oa/dedup/SparkCreateMergeRels.java | 5 +- 3 files changed, 158 insertions(+), 149 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java index ef296bfc90..027bf0735d 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java @@ -1,13 +1,7 @@ package eu.dnetlib.dhp.oozie; -import com.google.common.io.Resources; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import org.apache.commons.lang3.time.DurationFormatUtils; -import org.apache.commons.text.StringSubstitutor; -import org.apache.spark.SparkConf; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import java.net.URL; import java.nio.charset.StandardCharsets; @@ -15,7 +9,15 @@ import java.util.HashMap; import java.util.Map; import java.util.Optional; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import org.apache.commons.lang3.time.DurationFormatUtils; +import org.apache.commons.text.StringSubstitutor; +import org.apache.spark.SparkConf; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.common.io.Resources; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; public class RunSQLSparkJob { private static final Logger log = LoggerFactory.getLogger(RunSQLSparkJob.class); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index 4c12d1dc65..eddfba309d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -1,6 +1,16 @@ package eu.dnetlib.dhp.oa.dedup; +import java.util.*; +import java.util.stream.Stream; + +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 eu.dnetlib.dhp.oa.dedup.model.Identifier; import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.common.ModelSupport; @@ -8,180 +18,176 @@ 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; + public static final class DedupRecordReduceState { + public final String dedupId; - public final ArrayList aliases = new ArrayList<>(); + public final ArrayList aliases = new ArrayList<>(); - public final HashSet acceptanceDate = new HashSet<>(); + public final HashSet acceptanceDate = new HashSet<>(); - public OafEntity entity; + public OafEntity entity; - 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()); - } - } - } - } + 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()); + } + } + } + } - public String getDedupId() { - return dedupId; - } - } - private static final int MAX_ACCEPTANCE_DATE = 20; + public String getDedupId() { + return dedupId; + } + } - private DedupRecordFactory() { - } + private static final int MAX_ACCEPTANCE_DATE = 20; - public static Dataset createDedupRecord( - final SparkSession spark, - final DataInfo dataInfo, - final String mergeRelsInputPath, - final String entitiesInputPath, - final Class clazz) { + private DedupRecordFactory() { + } - final long ts = System.currentTimeMillis(); - final Encoder beanEncoder = Encoders.bean(clazz); - final Encoder kryoEncoder = Encoders.kryo(clazz); + public static Dataset createDedupRecord( + final SparkSession spark, + final DataInfo dataInfo, + final String mergeRelsInputPath, + final String entitiesInputPath, + final Class clazz) { - // - Dataset entities = spark - .read() - .schema(Encoders.bean(clazz).schema()) - .json(entitiesInputPath) - .as(beanEncoder) - .map( - (MapFunction>) entity -> { - return new Tuple2<>(entity.getId(), entity); - }, - Encoders.tuple(Encoders.STRING(), kryoEncoder)) - .selectExpr("_1 AS id", "_2 AS kryoObject"); + final long ts = System.currentTimeMillis(); + final Encoder beanEncoder = Encoders.bean(clazz); + final Encoder kryoEncoder = Encoders.kryo(clazz); - // : source is the dedup_id, target is the id of the mergedIn - Dataset mergeRels = spark - .read() - .load(mergeRelsInputPath) - .where("relClass == 'merges'") - .selectExpr("source as dedupId", "target as id"); + // + Dataset entities = spark + .read() + .schema(Encoders.bean(clazz).schema()) + .json(entitiesInputPath) + .as(beanEncoder) + .map( + (MapFunction>) entity -> { + return new Tuple2<>(entity.getId(), entity); + }, + Encoders.tuple(Encoders.STRING(), kryoEncoder)) + .selectExpr("_1 AS id", "_2 AS kryoObject"); - return mergeRels - .join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left") - .select("dedupId", "id", "kryoObject") - .as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder)) - .map((MapFunction, DedupRecordReduceState>) t -> new DedupRecordReduceState(t._1(), t._2(), t._3()), Encoders.kryo(DedupRecordReduceState.class)) - .groupByKey((MapFunction) DedupRecordReduceState::getDedupId, Encoders.STRING()) - .reduceGroups( - (ReduceFunction) (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); + // : source is the dedup_id, target is the id of the mergedIn + Dataset mergeRels = spark + .read() + .load(mergeRelsInputPath) + .where("relClass == 'merges'") + .selectExpr("source as dedupId", "target as id"); - return t1; - } - ) - .flatMap - ((FlatMapFunction, OafEntity>) t -> { - String dedupId = t._1(); - DedupRecordReduceState agg = t._2(); + return mergeRels + .join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left") + .select("dedupId", "id", "kryoObject") + .as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder)) + .map( + (MapFunction, DedupRecordReduceState>) t -> new DedupRecordReduceState( + t._1(), t._2(), t._3()), + Encoders.kryo(DedupRecordReduceState.class)) + .groupByKey( + (MapFunction) DedupRecordReduceState::getDedupId, Encoders.STRING()) + .reduceGroups( + (ReduceFunction) (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); - if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) { - return Collections.emptyIterator(); - } + return t1; + }) + .flatMap((FlatMapFunction, OafEntity>) t -> { + String dedupId = t._1(); + DedupRecordReduceState agg = t._2(); - 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); - } + if (agg.acceptanceDate.size() >= MAX_ACCEPTANCE_DATE) { + return Collections.emptyIterator(); + } - private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) { + 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; } + int compare = new IdentifierComparator<>() + .compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate)); - int compare = new IdentifierComparator<>() - .compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate)); - - if (compare > 0) { + if (compare > 0) { OafEntity swap = duplicate; - duplicate = entity; - entity = swap; - } + duplicate = entity; + entity = swap; + } - entity.mergeFrom(duplicate); + entity.mergeFrom(duplicate); - if (ModelSupport.isSubClass(duplicate, Result.class)) { - Result re = (Result) entity; - Result rd = (Result) duplicate; + if (ModelSupport.isSubClass(duplicate, Result.class)) { + Result re = (Result) entity; + Result rd = (Result) duplicate; - List> authors = new ArrayList<>(); - if (re.getAuthor() != null) { - authors.add(re.getAuthor()); - } - if (rd.getAuthor() != null) { - authors.add(rd.getAuthor()); - } + List> authors = new ArrayList<>(); + if (re.getAuthor() != null) { + authors.add(re.getAuthor()); + } + if (rd.getAuthor() != null) { + authors.add(rd.getAuthor()); + } - re.setAuthor(AuthorMerger.merge(authors)); - } + re.setAuthor(AuthorMerger.merge(authors)); + } - return entity; - } + return entity; + } - public static T entityMerger( - String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) { - T base = entities.next()._2(); + public static T entityMerger( + String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) { + T base = entities.next()._2(); - while (entities.hasNext()) { - T duplicate = entities.next()._2(); - if (duplicate != null) - base = (T) reduceEntity(base, duplicate); - } + 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); + base.setId(id); + base.setDataInfo(dataInfo); + base.setLastupdatetimestamp(ts); - return base; - } + return base; + } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java index 191870d3b0..59626c1414 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java @@ -242,13 +242,14 @@ public class SparkCreateMergeRels extends AbstractSparkAction { // this was a pivot in a previous graph but it has been merged into a new group with different // pivot - if (!r.isNullAt(r.fieldIndex("lastUsage")) && !pivot.equals(id) && !dedupId.equals(pivotDedupId)) { + if (!r.isNullAt(r.fieldIndex("lastUsage")) && !pivot.equals(id) + && !dedupId.equals(pivotDedupId)) { // materialize the previous dedup record as a merge relation with the new one res.add(new Tuple3<>(dedupId, pivotDedupId, null)); } // add merge relations - if (cut <=0 || r.getAs("position") <= cut) { + if (cut <= 0 || r. getAs("position") <= cut) { res.add(new Tuple3<>(id, pivotDedupId, pivot)); }