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Merge pull request 'Fill mergedIds field and filter mergerels with dedup records actually created' (#500) from mergedids into beta 

Reviewed-on: #500
This commit is contained in:
Claudio Atzori 2024-10-28 13:43:09 +01:00
parent 5916346ba1 56224e034a
commit 940735921f
2 changed files with 46 additions and 5 deletions
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15
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
View File

@ -2,14 +2,13 @@
package eu.dnetlib.dhp.oa.dedup;
import java.util.*;
import java.util.stream.Collectors;
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.FlatMapGroupsFunction;
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;
@ -107,6 +106,8 @@ public class DedupRecordFactory {
final HashSet<String> acceptanceDate = new HashSet<>();
boolean isVisible = false;
while (it.hasNext()) {
Tuple3<String, String, OafEntity> t = it.next();
OafEntity entity = t._3();
@ -114,6 +115,7 @@ public class DedupRecordFactory {
if (entity == null) {
aliases.add(t._2());
} else {
isVisible = isVisible || !entity.getDataInfo().getInvisible();
cliques.add(entity);
if (acceptanceDate.size() < MAX_ACCEPTANCE_DATE) {
@ -129,13 +131,20 @@ public class DedupRecordFactory {
}
if (acceptanceDate.size() >= MAX_ACCEPTANCE_DATE || cliques.isEmpty()) {
if (!isVisible || acceptanceDate.size() >= MAX_ACCEPTANCE_DATE || cliques.isEmpty()) {
return Collections.emptyIterator();
}
OafEntity mergedEntity = MergeUtils.mergeGroup(dedupId, cliques.iterator());
// dedup records do not have date of transformation attribute
mergedEntity.setDateoftransformation(null);
mergedEntity
.setMergedIds(
Stream
.concat(cliques.stream().map(OafEntity::getId), aliases.stream())
.distinct()
.sorted()
.collect(Collectors.toList()));
return Stream
.concat(

36
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
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@ -5,11 +5,11 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTION
import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVENANCE_DEDUP;
import java.io.IOException;
import java.util.Arrays;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.*;
import org.dom4j.DocumentException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -17,6 +17,7 @@ import org.xml.sax.SAXException;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
@ -25,6 +26,7 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import scala.collection.JavaConverters;
public class SparkCreateDedupRecord extends AbstractSparkAction {
@ -85,6 +87,36 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
log.info("Updating mergerels for: '{}'", subEntity);
final Dataset<Row> dedupIds = spark
.read()
.schema("`id` STRING, `mergedIds` ARRAY<STRING>")
.json(outputPath)
.selectExpr("id as source", "explode(mergedIds) as target");
spark
.read()
.load(mergeRelPath)
.where("relClass == 'merges'")
.join(dedupIds, JavaConverters.asScalaBuffer(Arrays.asList("source", "target")).toSeq(), "left_semi")
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.save(workingPath + "/mergerel_filtered");
final Dataset<Row> validRels = spark.read().load(workingPath + "/mergerel_filtered");
final Dataset<Row> filteredMergeRels = validRels
.union(
validRels
.withColumnRenamed("source", "source_tmp")
.withColumnRenamed("target", "target_tmp")
.withColumn("relClass", functions.lit(ModelConstants.IS_MERGED_IN))
.withColumnRenamed("target_tmp", "source")
.withColumnRenamed("source_tmp", "target"));
saveParquet(filteredMergeRels, mergeRelPath, SaveMode.Overwrite);
removeOutputDir(spark, workingPath + "/mergerel_filtered");
}
}