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implmented DispatchEntitiesApplication using spark2 datasets

This commit is contained in:
Claudio Atzori 2020-04-24 14:36:53 +02:00
parent 48157e0fc4
commit a3e480d1c9
1 changed files with 17 additions and 31 deletions
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48
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java
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@ -2,16 +2,18 @@ package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import java.util.Optional; import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
@ -20,8 +22,6 @@ public class DispatchEntitiesApplication {
private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class); private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws Exception { public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = final ArgumentApplicationParser parser =
new ArgumentApplicationParser( new ArgumentApplicationParser(
@ -45,15 +45,9 @@ public class DispatchEntitiesApplication {
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
removeOutputDir(spark, targetPath); removeOutputDir(spark, targetPath);
ModelSupport.oafTypes
processEntity(spark, Publication.class, sourcePath, targetPath); .values()
processEntity(spark, Dataset.class, sourcePath, targetPath); .forEach(clazz -> processEntity(spark, clazz, sourcePath, targetPath));
processEntity(spark, Software.class, sourcePath, targetPath);
processEntity(spark, OtherResearchProduct.class, sourcePath, targetPath);
processEntity(spark, Datasource.class, sourcePath, targetPath);
processEntity(spark, Organization.class, sourcePath, targetPath);
processEntity(spark, Project.class, sourcePath, targetPath);
processEntity(spark, Relation.class, sourcePath, targetPath);
}); });
} }
@ -64,26 +58,18 @@ public class DispatchEntitiesApplication {
final String targetPath) { final String targetPath) {
final String type = clazz.getSimpleName().toLowerCase(); final String type = clazz.getSimpleName().toLowerCase();
log.info(String.format("Processing entities (%s) in file: %s", type, sourcePath)); log.info("Processing entities ({}) in file: {}", type, sourcePath);
/*
spark.read() spark.read()
.textFile(sourcePath)
.filter((FilterFunction<String>) value -> isEntityType(value, type))
.map((MapFunction<String, String>) value -> StringUtils.substringAfter(value, "|"), Encoders.STRING())
.map((MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.parquet(targetPath + "/" + type);
*/
JavaSparkContext.fromSparkContext(spark.sparkContext())
.textFile(sourcePath) .textFile(sourcePath)
.filter(l -> isEntityType(l, type)) .filter((FilterFunction<String>) value -> isEntityType(value, type))
.map(l -> StringUtils.substringAfter(l, "|")) .map(
.saveAsTextFile( (MapFunction<String, String>) l -> StringUtils.substringAfter(l, "|"),
targetPath + "/" + type, GzipCodec.class); // use repartition(XXX) ??? Encoders.STRING())
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.text(targetPath + "/" + type);
} }
private static boolean isEntityType(final String line, final String type) { private static boolean isEntityType(final String line, final String type) {