128 lines
4.2 KiB
Java
128 lines
4.2 KiB
Java
|
|
package eu.dnetlib.dhp.oa.graph.raw;
|
|
|
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
|
|
|
import java.io.FileNotFoundException;
|
|
import java.util.Objects;
|
|
import java.util.Optional;
|
|
|
|
import org.apache.commons.io.IOUtils;
|
|
import org.apache.spark.SparkConf;
|
|
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.SaveMode;
|
|
import org.apache.spark.sql.SparkSession;
|
|
import org.slf4j.Logger;
|
|
import org.slf4j.LoggerFactory;
|
|
|
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
|
import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
|
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
import scala.Tuple2;
|
|
|
|
public class PatchRelationsApplication {
|
|
|
|
private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.class);
|
|
|
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
|
|
|
public static void main(final String[] args) throws Exception {
|
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
|
IOUtils
|
|
.toString(
|
|
Optional
|
|
.ofNullable(
|
|
PatchRelationsApplication.class
|
|
.getResourceAsStream(
|
|
"/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
|
|
.orElseThrow(FileNotFoundException::new)));
|
|
parser.parseArgument(args);
|
|
|
|
final Boolean isSparkSessionManaged = Optional
|
|
.ofNullable(parser.get("isSparkSessionManaged"))
|
|
.map(Boolean::valueOf)
|
|
.orElse(Boolean.TRUE);
|
|
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
|
|
|
final String graphBasePath = parser.get("graphBasePath");
|
|
log.info("graphBasePath: {}", graphBasePath);
|
|
|
|
final String workingDir = parser.get("workingDir");
|
|
log.info("workingDir: {}", workingDir);
|
|
|
|
final String idMappingPath = parser.get("idMappingPath");
|
|
log.info("idMappingPath: {}", idMappingPath);
|
|
|
|
final SparkConf conf = new SparkConf();
|
|
runWithSparkSession(
|
|
conf,
|
|
isSparkSessionManaged,
|
|
spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
|
|
}
|
|
|
|
/**
|
|
* Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the
|
|
* mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location.
|
|
*
|
|
* @param spark the SparkSession
|
|
* @param graphBasePath base graph path providing the set of relations to patch
|
|
* @param workingDir intermediate storage location
|
|
* @param idMappingPath dataset providing the old -> new identifier mapping
|
|
*/
|
|
private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir,
|
|
final String idMappingPath) {
|
|
|
|
final String relationPath = graphBasePath + "/relation";
|
|
|
|
final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
|
|
final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
|
|
|
|
log.info("relations: {}", rels.count());
|
|
log.info("idMapping: {}", idMapping.count());
|
|
|
|
final Dataset<Relation> bySource = rels
|
|
.joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
|
|
.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
|
|
final Relation r = t._1();
|
|
Optional
|
|
.ofNullable(t._2())
|
|
.map(RelationIdMapping::getNewId)
|
|
.ifPresent(r::setSource);
|
|
return r;
|
|
}, Encoders.bean(Relation.class));
|
|
|
|
bySource
|
|
.joinWith(idMapping, bySource.col("target").equalTo(idMapping.col("oldId")), "left")
|
|
.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
|
|
final Relation r = t._1();
|
|
Optional
|
|
.ofNullable(t._2())
|
|
.map(RelationIdMapping::getNewId)
|
|
.ifPresent(r::setTarget);
|
|
return r;
|
|
}, Encoders.bean(Relation.class))
|
|
.map(
|
|
(MapFunction<Relation, String>) OBJECT_MAPPER::writeValueAsString,
|
|
Encoders.STRING())
|
|
.write()
|
|
.mode(SaveMode.Overwrite)
|
|
.option("compression", "gzip")
|
|
.text(workingDir);
|
|
|
|
spark
|
|
.read()
|
|
.textFile(workingDir)
|
|
.write()
|
|
.mode(SaveMode.Overwrite)
|
|
.option("compression", "gzip")
|
|
.text(relationPath);
|
|
}
|
|
|
|
}
|