137 lines
4.9 KiB
Java
137 lines
4.9 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.schema.oaf.*;
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/**
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* It selects the valid relations among those present in the graph. One relation is valid if it is not deletedbyinference
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* and if both the source and the target node are present in the graph and are not deleted by inference nor invisible.
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* To check this I made a view of the ids of all the entities in the graph, and select the relations for which a join exists
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* with this view for both the source and the target
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*/
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public class SparkSelectValidRelationsJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SparkSelectValidRelationsJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Utils.removeOutputDir(spark, outputPath);
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selectValidRelation(spark, inputPath, outputPath);
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});
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}
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private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) {
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Dataset<Relation> relation = Utils.readPath(spark, inputPath + "/relation", Relation.class);
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Dataset<Publication> publication = Utils.readPath(spark, inputPath + "/publication", Publication.class);
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Dataset<eu.dnetlib.dhp.schema.oaf.Dataset> dataset = Utils
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.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
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Dataset<Software> software = Utils.readPath(spark, inputPath + "/software", Software.class);
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Dataset<OtherResearchProduct> other = Utils
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.readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class);
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Dataset<Organization> organization = Utils.readPath(spark, inputPath + "/organization", Organization.class);
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Dataset<Project> project = Utils.readPath(spark, inputPath + "/project", Project.class);
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Dataset<Datasource> datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class);
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relation.createOrReplaceTempView("relation");
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publication.createOrReplaceTempView("publication");
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dataset.createOrReplaceTempView("dataset");
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other.createOrReplaceTempView("other");
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software.createOrReplaceTempView("software");
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organization.createOrReplaceTempView("organization");
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project.createOrReplaceTempView("project");
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datasource.createOrReplaceTempView("datasource");
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spark
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.sql(
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"SELECT id " +
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"FROM publication " +
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"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
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"UNION ALL " +
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"SELECT id " +
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"FROM dataset " +
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"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
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"UNION ALL " +
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"SELECT id " +
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"FROM other " +
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"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
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"UNION ALL " +
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"SELECT id " +
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"FROM software " +
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"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
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"UNION ALL " +
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"SELECT id " +
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"FROM organization " +
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"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
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"UNION ALL " +
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"SELECT id " +
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"FROM project " +
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"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
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"UNION ALL " +
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"SELECT id " +
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"FROM datasource " +
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"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false ")
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.createOrReplaceTempView("identifiers");
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spark
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.sql(
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"SELECT relation.* " +
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"FROM relation " +
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"JOIN identifiers i1 " +
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"ON source = i1.id " +
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"JOIN identifiers i2 " +
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"ON target = i2.id " +
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"WHERE datainfo.deletedbyinference = false")
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.as(Encoders.bean(Relation.class))
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.json(outputPath);
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}
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}
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