forked from D-Net/dnet-hadoop
code formatting
This commit is contained in:
parent
db8b90a156
commit
1781609508
|
|
@ -1,11 +1,11 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.merge;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
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;
|
||||
|
|
@ -16,13 +16,16 @@ 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.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
/**
|
||||
* Combines the content from two aggregator graph tables of the same type, entities (or relationships) with the same ids
|
||||
* are picked preferring those from the BETA aggregator rather then from PROD. The identity of a relationship is defined
|
||||
|
|
@ -30,101 +33,102 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
|||
*/
|
||||
public class MergeGraphSparkJob {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJob.class);
|
||||
private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJob.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
CleanGraphSparkJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/merge_graphs_parameters.json"));
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
CleanGraphSparkJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/merge_graphs_parameters.json"));
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
String betaInputPath = parser.get("betaInputPath");
|
||||
log.info("betaInputPath: {}", betaInputPath);
|
||||
String betaInputPath = parser.get("betaInputPath");
|
||||
log.info("betaInputPath: {}", betaInputPath);
|
||||
|
||||
String prodInputPath = parser.get("prodInputPath");
|
||||
log.info("prodInputPath: {}", prodInputPath);
|
||||
String prodInputPath = parser.get("prodInputPath");
|
||||
log.info("prodInputPath: {}", prodInputPath);
|
||||
|
||||
String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
String graphTableClassName = parser.get("graphTableClassName");
|
||||
log.info("graphTableClassName: {}", graphTableClassName);
|
||||
String graphTableClassName = parser.get("graphTableClassName");
|
||||
log.info("graphTableClassName: {}", graphTableClassName);
|
||||
|
||||
Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
|
||||
Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
mergeGraphTable(spark, betaInputPath, prodInputPath, entityClazz, entityClazz, outputPath);
|
||||
});
|
||||
}
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
mergeGraphTable(spark, betaInputPath, prodInputPath, entityClazz, entityClazz, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static <P extends Oaf, B extends Oaf> void mergeGraphTable(
|
||||
SparkSession spark,
|
||||
String betaInputPath,
|
||||
String prodInputPath,
|
||||
Class<P> p_clazz,
|
||||
Class<B> b_clazz,
|
||||
String outputPath) {
|
||||
private static <P extends Oaf, B extends Oaf> void mergeGraphTable(
|
||||
SparkSession spark,
|
||||
String betaInputPath,
|
||||
String prodInputPath,
|
||||
Class<P> p_clazz,
|
||||
Class<B> b_clazz,
|
||||
String outputPath) {
|
||||
|
||||
Dataset<Tuple2<String, B>> beta = readTableFromPath(spark, betaInputPath, b_clazz);
|
||||
Dataset<Tuple2<String, P>> prod = readTableFromPath(spark, prodInputPath, p_clazz);
|
||||
Dataset<Tuple2<String, B>> beta = readTableFromPath(spark, betaInputPath, b_clazz);
|
||||
Dataset<Tuple2<String, P>> prod = readTableFromPath(spark, prodInputPath, p_clazz);
|
||||
|
||||
prod.joinWith(beta, prod.col("_1").equalTo(beta.col("_1")), "full_outer")
|
||||
.map((MapFunction<Tuple2<Tuple2<String, P>, Tuple2<String, B>>, P>) value -> {
|
||||
Optional<P> p = Optional.ofNullable(value._1()).map(Tuple2::_2);
|
||||
Optional<B> b = Optional.ofNullable(value._2()).map(Tuple2::_2);
|
||||
if (p.isPresent() & !b.isPresent()) {
|
||||
return p.get();
|
||||
}
|
||||
if (b.isPresent()) {
|
||||
return (P) b.get();
|
||||
}
|
||||
return null;
|
||||
}, Encoders.bean(p_clazz))
|
||||
.filter((FilterFunction<P>) Objects::nonNull)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
prod
|
||||
.joinWith(beta, prod.col("_1").equalTo(beta.col("_1")), "full_outer")
|
||||
.map((MapFunction<Tuple2<Tuple2<String, P>, Tuple2<String, B>>, P>) value -> {
|
||||
Optional<P> p = Optional.ofNullable(value._1()).map(Tuple2::_2);
|
||||
Optional<B> b = Optional.ofNullable(value._2()).map(Tuple2::_2);
|
||||
if (p.isPresent() & !b.isPresent()) {
|
||||
return p.get();
|
||||
}
|
||||
if (b.isPresent()) {
|
||||
return (P) b.get();
|
||||
}
|
||||
return null;
|
||||
}, Encoders.bean(p_clazz))
|
||||
.filter((FilterFunction<P>) Objects::nonNull)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
private static <T extends Oaf> Dataset<Tuple2<String, T>> readTableFromPath(
|
||||
SparkSession spark, String inputEntityPath, Class<T> clazz) {
|
||||
private static <T extends Oaf> Dataset<Tuple2<String, T>> readTableFromPath(
|
||||
SparkSession spark, String inputEntityPath, Class<T> clazz) {
|
||||
|
||||
log.info("Reading Graph table from: {}", inputEntityPath);
|
||||
return spark
|
||||
.read()
|
||||
.textFile(inputEntityPath)
|
||||
.map(
|
||||
(MapFunction<String, Tuple2<String, T>>) value -> {
|
||||
final T t = OBJECT_MAPPER.readValue(value, clazz);
|
||||
final String id = ModelSupport.idFn().apply(t);
|
||||
return new Tuple2<>(id, t);
|
||||
},
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
|
||||
}
|
||||
log.info("Reading Graph table from: {}", inputEntityPath);
|
||||
return spark
|
||||
.read()
|
||||
.textFile(inputEntityPath)
|
||||
.map(
|
||||
(MapFunction<String, Tuple2<String, T>>) value -> {
|
||||
final T t = OBJECT_MAPPER.readValue(value, clazz);
|
||||
final String id = ModelSupport.idFn().apply(t);
|
||||
return new Tuple2<>(id, t);
|
||||
},
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
|
||||
}
|
||||
|
||||
private static void removeOutputDir(SparkSession spark, String path) {
|
||||
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
|
||||
}
|
||||
private static void removeOutputDir(SparkSession spark, String path) {
|
||||
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue