103 lines
3.6 KiB
Java
103 lines
3.6 KiB
Java
|
|
package eu.dnetlib.dedup.sx;
|
|
|
|
import java.io.IOException;
|
|
|
|
import org.apache.commons.io.IOUtils;
|
|
import org.apache.hadoop.io.compress.GzipCodec;
|
|
import org.apache.spark.api.java.JavaPairRDD;
|
|
import org.apache.spark.api.java.JavaRDD;
|
|
import org.apache.spark.api.java.JavaSparkContext;
|
|
import org.apache.spark.api.java.function.PairFunction;
|
|
import org.apache.spark.sql.*;
|
|
|
|
import com.fasterxml.jackson.databind.DeserializationFeature;
|
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset;
|
|
import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication;
|
|
import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown;
|
|
import eu.dnetlib.dhp.utils.DHPUtils;
|
|
import scala.Tuple2;
|
|
|
|
public class SparkUpdateEntityJob {
|
|
|
|
static final String IDJSONPATH = "$.id";
|
|
|
|
public static void main(String[] args) throws Exception {
|
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
|
IOUtils
|
|
.toString(
|
|
SparkUpdateEntityJob.class
|
|
.getResourceAsStream(
|
|
"/eu/dnetlib/dhp/sx/dedup/dedup_delete_by_inference_parameters.json")));
|
|
parser.parseArgument(args);
|
|
final SparkSession spark = SparkSession
|
|
.builder()
|
|
.appName(SparkUpdateEntityJob.class.getSimpleName())
|
|
.master(parser.get("master"))
|
|
.getOrCreate();
|
|
|
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
|
final String entityPath = parser.get("entityPath");
|
|
final String mergeRelPath = parser.get("mergeRelPath");
|
|
final String dedupRecordPath = parser.get("dedupRecordPath");
|
|
final String entity = parser.get("entity");
|
|
final String destination = parser.get("targetPath");
|
|
|
|
final Dataset<Relation> df = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class));
|
|
final JavaPairRDD<String, String> mergedIds = df
|
|
.where("relClass == 'merges'")
|
|
.select(df.col("target"))
|
|
.distinct()
|
|
.toJavaRDD()
|
|
.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
|
|
final JavaRDD<String> sourceEntity = sc.textFile(entityPath);
|
|
|
|
final JavaRDD<String> dedupEntity = sc.textFile(dedupRecordPath);
|
|
JavaPairRDD<String, String> entitiesWithId = sourceEntity
|
|
.mapToPair(
|
|
(PairFunction<String, String, String>) s -> new Tuple2<>(DHPUtils.getJPathString(IDJSONPATH, s), s));
|
|
Class<? extends Oaf> mainClass;
|
|
switch (entity) {
|
|
case "publication":
|
|
mainClass = DLIPublication.class;
|
|
break;
|
|
case "dataset":
|
|
mainClass = DLIDataset.class;
|
|
break;
|
|
case "unknown":
|
|
mainClass = DLIUnknown.class;
|
|
break;
|
|
default:
|
|
throw new IllegalArgumentException("Illegal type " + entity);
|
|
}
|
|
JavaRDD<String> map = entitiesWithId
|
|
.leftOuterJoin(mergedIds)
|
|
.map(
|
|
k -> k._2()._2().isPresent()
|
|
? updateDeletedByInference(k._2()._1(), mainClass)
|
|
: k._2()._1());
|
|
map.union(dedupEntity).saveAsTextFile(destination, GzipCodec.class);
|
|
}
|
|
|
|
private static <T extends Oaf> String updateDeletedByInference(
|
|
final String json, final Class<T> clazz) {
|
|
final ObjectMapper mapper = new ObjectMapper();
|
|
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
|
try {
|
|
Oaf entity = mapper.readValue(json, clazz);
|
|
if (entity.getDataInfo() == null)
|
|
entity.setDataInfo(new DataInfo());
|
|
entity.getDataInfo().setDeletedbyinference(true);
|
|
return mapper.writeValueAsString(entity);
|
|
} catch (IOException e) {
|
|
throw new RuntimeException("Unable to convert json", e);
|
|
}
|
|
}
|
|
}
|