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[DUMP DELTA PROJECTS] refactoring

This commit is contained in:
Miriam Baglioni 2022-06-27 18:07:58 +02:00
parent 1d1fe3b151
commit 71744a1f52
1 changed files with 60 additions and 61 deletions
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121
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java
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@ -1,80 +1,79 @@
package eu.dnetlib.dhp.oa.graph.dump.projectssubset; package eu.dnetlib.dhp.oa.graph.dump.projectssubset;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable; import java.io.Serializable;
import java.util.List;
import java.util.Objects; import java.util.Objects;
import java.util.Optional; import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.community.Funder;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; import eu.dnetlib.dhp.schema.dump.oaf.graph.Project;
import scala.Tuple2; import scala.Tuple2;
public class ProjectsSubsetSparkJob implements Serializable { public class ProjectsSubsetSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils public static void main(String[] args) throws Exception {
.toString( String jsonConfiguration = IOUtils
ProjectsSubsetSparkJob.class .toString(
.getResourceAsStream( ProjectsSubsetSparkJob.class
"/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); .getResourceAsStream(
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json"));
parser.parseArgument(args); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
Boolean isSparkSessionManaged = Optional parser.parseArgument(args);
.ofNullable(parser.get("isSparkSessionManaged")) Boolean isSparkSessionManaged = Optional
.map(Boolean::valueOf) .ofNullable(parser.get("isSparkSessionManaged"))
.orElse(Boolean.TRUE); .map(Boolean::valueOf)
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); .orElse(Boolean.TRUE);
final String inputPath = parser.get("sourcePath"); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
log.info("inputPath: {}", inputPath); final String inputPath = parser.get("sourcePath");
final String outputPath = parser.get("outputPath"); log.info("inputPath: {}", inputPath);
log.info("outputPath: {}", outputPath); final String outputPath = parser.get("outputPath");
final String projectListPath = parser.get("projectListPath"); log.info("outputPath: {}", outputPath);
log.info("projectListPath: {}", projectListPath); final String projectListPath = parser.get("projectListPath");
SparkConf conf = new SparkConf(); log.info("projectListPath: {}", projectListPath);
runWithSparkSession( SparkConf conf = new SparkConf();
conf, runWithSparkSession(
isSparkSessionManaged, conf,
spark -> { isSparkSessionManaged,
Utils.removeOutputDir(spark, outputPath); spark -> {
getNewProjectList(spark, inputPath, outputPath, projectListPath); Utils.removeOutputDir(spark, outputPath);
}); getNewProjectList(spark, inputPath, outputPath, projectListPath);
} });
private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, }
String projectListPath) {
Dataset<String> projectList = spark.read().textFile(projectListPath); private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath,
// projectList.show(false); String projectListPath) {
Dataset<Project> projects; Dataset<String> projectList = spark.read().textFile(projectListPath);
projects = Utils.readPath(spark, inputPath, Project.class); Dataset<Project> projects;
projects projects = Utils.readPath(spark, inputPath, Project.class);
.joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") projects
.map((MapFunction<Tuple2<Project, String>, Project>) t2 -> { .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left")
if (Optional.ofNullable(t2._2()).isPresent()) .map((MapFunction<Tuple2<Project, String>, Project>) t2 -> {
return null; if (Optional.ofNullable(t2._2()).isPresent())
return t2._1(); return null;
}, Encoders.bean(Project.class)) return t2._1();
.filter(Objects::nonNull) }, Encoders.bean(Project.class))
.write() .filter(Objects::nonNull)
.mode(SaveMode.Overwrite) .write()
.option("compression", "gzip") .mode(SaveMode.Overwrite)
.json(outputPath); .option("compression", "gzip")
Utils .json(outputPath);
.readPath(spark, outputPath, Project.class) Utils
.map((MapFunction<Project, String>) p -> p.getId(), Encoders.STRING()) .readPath(spark, outputPath, Project.class)
.write() .map((MapFunction<Project, String>) p -> p.getId(), Encoders.STRING())
.mode(SaveMode.Append) .write()
.option("compression", "gzip") .mode(SaveMode.Append)
.text(projectListPath); .option("compression", "gzip")
} .text(projectListPath);
} }
}