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added logic to select only the valid relations: those not deletedbyinference and having both part of the relation as entities in the graph

This commit is contained in:
Miriam Baglioni 2021-07-13 15:20:39 +02:00
parent 13c66e16be
commit 9a58f1b93d
1 changed files with 127 additions and 0 deletions
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dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java Normal file
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package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.oaf.*;
public class SparkSelectValidRelationsJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkSelectValidRelationsJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_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);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
selectValidRelation(spark, inputPath, outputPath);
});
}
private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) {
Dataset<Relation> relation = Utils.readPath(spark, inputPath + "/relation", Relation.class);
Dataset<Publication> publication = Utils.readPath(spark, inputPath + "/publication", Publication.class);
Dataset<eu.dnetlib.dhp.schema.oaf.Dataset> dataset = Utils
.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
Dataset<Software> software = Utils.readPath(spark, inputPath + "/software", Software.class);
Dataset<OtherResearchProduct> other = Utils
.readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class);
Dataset<Organization> organization = Utils.readPath(spark, inputPath + "/organization", Organization.class);
Dataset<Project> project = Utils.readPath(spark, inputPath + "/project", Project.class);
Dataset<Datasource> datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class);
relation.createOrReplaceTempView("relation");
publication.createOrReplaceTempView("publication");
dataset.createOrReplaceTempView("dataset");
other.createOrReplaceTempView("other");
software.createOrReplaceTempView("software");
organization.createOrReplaceTempView("organization");
project.createOrReplaceTempView("project");
datasource.createOrReplaceTempView("datasource");
spark
.sql(
"SELECT id " +
"FROM publication " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM dataset " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM other " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM software " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM organization " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM project " +
"UNION ALL " +
"SELECT id " +
"FROM datasource ")
.createOrReplaceTempView("identifiers");
spark
.sql(
"SELECT relation.* " +
"FROM relation " +
"JOIN identifiers i1 " +
"ON source = i1.id " +
"JOIN identifiers i2 " +
"ON target = i2.id " +
"WHERE datainfo.deletedbyinference = false")
.as(Encoders.bean(Relation.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
;
}
}