package eu.dnetlib.dhp.oa.dedup; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import scala.Tuple2; import java.io.IOException; import java.util.List; public class SparkCreateSimRels extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class); public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); } public static void main(String[] args) throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString( SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); parser.parseArgument(args); new SparkCreateSimRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override public void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException { //read oozie parameters final String graphBasePath = parser.get("graphBasePath"); final String isLookUpUrl = parser.get("isLookUpUrl"); final String actionSetId = parser.get("actionSetId"); final String workingPath = parser.get("workingPath"); System.out.println(String.format("graphBasePath: '%s'", graphBasePath)); System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl)); System.out.println(String.format("actionSetId: '%s'", actionSetId)); System.out.println(String.format("workingPath: '%s'", workingPath)); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); //for each dedup configuration for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) { final String entity = dedupConf.getWf().getEntityType(); final String subEntity = dedupConf.getWf().getSubEntityValue(); System.out.println(String.format("Creating simrels for: '%s'", subEntity)); JavaPairRDD mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity)) .mapToPair((PairFunction) s -> { MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); return new Tuple2(d.getIdentifier(), d); }); //create blocks for deduplication JavaPairRDD> blocks = Deduper.createSortedBlocks(sc, mapDocument, dedupConf); //create relations by comparing only elements in the same group final JavaPairRDD dedupRels = Deduper.computeRelations(sc, blocks, dedupConf); JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity)); //save the simrel in the workingdir spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)) .write() .mode("overwrite") .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)); } } /** * Utility method used to create an atomic action from a Relation object * @param relation input relation * @return A tuple2 with [id, json serialization of the atomic action] * @throws JsonProcessingException */ public Tuple2 createSequenceFileRow(Relation relation) throws JsonProcessingException { ObjectMapper mapper = new ObjectMapper(); String id = relation.getSource() + "@" + relation.getRelClass() + "@" + relation.getTarget(); AtomicAction aa = new AtomicAction<>(Relation.class, relation); return new Tuple2<>( new Text(id), new Text(mapper.writeValueAsString(aa)) ); } public Relation createSimRel(String source, String target, String entity){ final Relation r = new Relation(); r.setSource(source); r.setTarget(target); switch(entity){ case "result": r.setRelClass("resultResult_dedupSimilarity_isSimilarTo"); break; case "organization": r.setRelClass("organizationOrganization_dedupSimilarity_isSimilarTo"); break; default: r.setRelClass("isSimilarTo"); break; } return r; } }