package eu.dnetlib.dhp.oa.graph.dump.complete; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.*; import org.apache.commons.io.IOUtils; 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.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.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.Provenance; import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; /** * Dumps eu.dnetlib.dhp.schema.oaf.Relation in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation */ public class SparkDumpRelationJob implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpRelationJob.class); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( SparkDumpRelationJob.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/dump/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); Optional rs = Optional.ofNullable(parser.get("removeSet")); final Set removeSet = new HashSet<>(); if (rs.isPresent()) { Collections.addAll(removeSet, rs.get().split(";")); } SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); dumpRelation(spark, inputPath, outputPath, removeSet); }); } private static void dumpRelation(SparkSession spark, String inputPath, String outputPath, Set removeSet) { Dataset relations = Utils.readPath(spark, inputPath, Relation.class); relations .filter((FilterFunction) r -> !removeSet.contains(r.getRelClass())) .map((MapFunction) relation -> { eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); relNew .setSource( Node .newInstance( relation.getSource(), ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2)))); relNew .setTarget( Node .newInstance( relation.getTarget(), ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2)))); relNew .setReltype( RelType .newInstance( relation.getRelClass(), relation.getSubRelType())); Optional odInfo = Optional.ofNullable(relation.getDataInfo()); if (odInfo.isPresent()) { DataInfo dInfo = odInfo.get(); if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { relNew .setProvenance( Provenance .newInstance( dInfo.getProvenanceaction().getClassname(), dInfo.getTrust())); } } if (Boolean.TRUE.equals(relation.getValidated())) { relNew.setValidated(relation.getValidated()); relNew.setValidationDate(relation.getValidationDate()); } return relNew; }, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) .write() .option("compression", "gzip") .mode(SaveMode.Overwrite) .json(outputPath); } }