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reading graph dump as text files, encoded as newline-delimited JSON records, as indicated in the wiki

This commit is contained in:
Claudio Atzori 2020-03-10 17:19:17 +01:00
parent 60aedb1110
commit 7b6f0c8756
1 changed files with 14 additions and 11 deletions
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25
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java
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@ -3,7 +3,7 @@ package eu.dnetlib.dhp.graph;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
@ -13,7 +13,9 @@ public class SparkGraphImporterJob {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGraphImporterJob.class.getResourceAsStream("/eu/dnetlib/dhp/graph/input_graph_parameters.json")));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils.toString(SparkGraphImporterJob.class.getResourceAsStream(
"/eu/dnetlib/dhp/graph/input_graph_parameters.json")));
parser.parseArgument(args);
try(SparkSession spark = getSparkSession(parser)) {
@ -26,23 +28,24 @@ public class SparkGraphImporterJob {
spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName));
// Read the input file and convert it into RDD of serializable object
GraphMappingUtils.types.forEach((name, clazz) -> {
spark.createDataset(sc.sequenceFile(inputPath + "/" + name, Text.class, Text.class)
.map(s -> new ObjectMapper().readValue(s._2().toString(), clazz))
.rdd(), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.saveAsTable(hiveDbName + "." + name);
});
GraphMappingUtils.types.forEach((name, clazz) -> spark.createDataset(sc.textFile(inputPath + "/" + name)
.map(s -> new ObjectMapper().readValue(s, clazz))
.rdd(), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.saveAsTable(hiveDbName + "." + name));
}
}
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
return SparkSession
.builder()
.appName(SparkGraphImporterJob.class.getSimpleName())
.master(parser.get("master"))
.config("hive.metastore.uris", parser.get("hive_metastore_uris"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
}