136 lines
4.2 KiB
Java
136 lines
4.2 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.Collections;
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import java.util.HashSet;
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import java.util.Optional;
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import java.util.Set;
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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.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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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.oa.model.Provenance;
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import eu.dnetlib.dhp.oa.model.graph.Node;
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import eu.dnetlib.dhp.oa.model.graph.RelType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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/**
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* Dumps eu.dnetlib.dhp.schema.oaf.Relation in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation
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*/
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public class SparkDumpRelationJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkDumpRelationJob.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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SparkDumpRelationJob.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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Optional<String> rs = Optional.ofNullable(parser.get("removeSet"));
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final Set<String> removeSet = new HashSet<>();
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if (rs.isPresent()) {
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Collections.addAll(removeSet, rs.get().split(";"));
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}
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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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dumpRelation(spark, inputPath, outputPath, removeSet);
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});
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}
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private static void dumpRelation(SparkSession spark, String inputPath, String outputPath, Set<String> removeSet) {
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Dataset<Relation> relations = Utils.readPath(spark, inputPath, Relation.class);
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relations
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.filter((FilterFunction<Relation>) r -> !removeSet.contains(r.getRelClass()))
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.map((MapFunction<Relation, eu.dnetlib.dhp.oa.model.graph.Relation>) relation -> {
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eu.dnetlib.dhp.oa.model.graph.Relation relNew = new eu.dnetlib.dhp.oa.model.graph.Relation();
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relNew
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.setSource(
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Node
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.newInstance(
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relation.getSource(),
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ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2))));
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relNew
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.setTarget(
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Node
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.newInstance(
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relation.getTarget(),
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ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2))));
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relNew
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.setReltype(
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RelType
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.newInstance(
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relation.getRelClass(),
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relation.getSubRelType()));
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Optional<DataInfo> odInfo = Optional.ofNullable(relation.getDataInfo());
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if (odInfo.isPresent()) {
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DataInfo dInfo = odInfo.get();
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if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() &&
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Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) {
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relNew
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.setProvenance(
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Provenance
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.newInstance(
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dInfo.getProvenanceaction().getClassname(),
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dInfo.getTrust()));
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}
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}
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if (Boolean.TRUE.equals(relation.getValidated())) {
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relNew.setValidated(relation.getValidated());
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relNew.setValidationDate(relation.getValidationDate());
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}
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return relNew;
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}, Encoders.bean(eu.dnetlib.dhp.oa.model.graph.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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