new implementation with one more serialization step

This commit is contained in:
Miriam Baglioni 2020-05-07 09:57:49 +02:00
parent dd2e698a72
commit 42ad51577a
2 changed files with 177 additions and 0 deletions

View File

@ -0,0 +1,145 @@
package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
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.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.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
import scala.Tuple2;
public class SparkCountryPropagationJob3 {
private static final Logger log = LoggerFactory.getLogger(SparkCountryPropagationJob3.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkCountryPropagationJob3.class
.getResourceAsStream(
"/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final Boolean saveGraph = Optional
.ofNullable(parser.get("saveGraph"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("saveGraph: {}", saveGraph);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
execPropagation(
spark,
inputPath,
outputPath,
resultClazz,
saveGraph);
});
}
private static <R extends Result> void execPropagation(
SparkSession spark,
String inputPath,
String outputPath,
Class<R> resultClazz,
boolean saveGraph) {
if (saveGraph) {
// updateResultTable(spark, potentialUpdates, inputPath, resultClazz, outputPath);
log.info("Reading Graph table from: {}", inputPath);
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaPairRDD<String, R> results = sc
.textFile(inputPath)
.map(r -> OBJECT_MAPPER.readValue(r, resultClazz))
.mapToPair(r -> new Tuple2<>(r.getId(), r));
JavaPairRDD<String, R> tmp = results.reduceByKey((r1, r2) -> {
if (r1 == null) {
return r2;
}
if (r2 == null) {
return r1;
}
if (Optional.ofNullable(r1.getCollectedfrom()).isPresent()) {
r1.setCountry(getUnionCountries(r1.getCountry(), r2.getCountry()));
return r1;
}
if (Optional.ofNullable(r2.getCollectedfrom()).isPresent()) {
r2.setCountry(getUnionCountries(r1.getCountry(), r2.getCountry()));
return r2;
}
r1.setCountry(getUnionCountries(r1.getCountry(), r2.getCountry()));
return r1;
});
tmp
.map(c -> c._2())
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
.saveAsTextFile(outputPath, GzipCodec.class);
}
}
private static List<Country> getUnionCountries(List<Country> country, List<Country> country1) {
HashSet<String> countries = country
.stream()
.map(c -> c.getClassid())
.collect(Collectors.toCollection(HashSet::new));
country
.addAll(
country1
.stream()
.filter(c -> !(countries.contains(c.getClassid())))
.collect(Collectors.toList()));
return country;
}
}

View File

@ -0,0 +1,32 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName":"h",
"paramLongName":"hive_metastore_uris",
"paramDescription": "the hive metastore uris",
"paramRequired": true
},
{
"paramName":"tn",
"paramLongName":"resultTableName",
"paramDescription": "the name of the result table we are currently working on",
"paramRequired": true
},
{
"paramName": "p",
"paramLongName": "preparedInfoPath",
"paramDescription": "the path where prepared info have been stored",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
}
]