119 lines
4.8 KiB
Java
119 lines
4.8 KiB
Java
package eu.dnetlib.dhp.oa.dedup;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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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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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.config.DedupConfig;
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import eu.dnetlib.pace.model.MapDocument;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.PairFunction;
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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.dom4j.DocumentException;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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import java.io.IOException;
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import java.util.List;
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public class SparkCreateSimRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
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public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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public static void main(String[] args) throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(
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SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
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parser.parseArgument(args);
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new SparkCreateSimRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@Override
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public void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException {
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//read oozie parameters
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final String graphBasePath = parser.get("graphBasePath");
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final String isLookUpUrl = parser.get("isLookUpUrl");
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final String actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("isLookUpUrl: '{}'", isLookUpUrl);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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//for each dedup configuration
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for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) {
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final String entity = dedupConf.getWf().getEntityType();
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final String subEntity = dedupConf.getWf().getSubEntityValue();
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log.info("Creating simrels for: '{}'", subEntity);
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final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
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removeOutputDir(spark, outputPath);
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JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.mapToPair((PairFunction<String, String, MapDocument>) s -> {
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MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
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return new Tuple2<>(d.getIdentifier(), d);
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});
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//create blocks for deduplication
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JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createSortedBlocks(sc, mapDocument, dedupConf);
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//create relations by comparing only elements in the same group
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final JavaPairRDD<String, String> dedupRels = Deduper.computeRelations(sc, blocks, dedupConf);
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JavaRDD<Relation> relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity));
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//save the simrel in the workingdir
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spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class))
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.write()
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.mode(SaveMode.Append)
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.save(outputPath);
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}
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}
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public Relation createSimRel(String source, String target, String entity) {
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final Relation r = new Relation();
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r.setSource(source);
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r.setTarget(target);
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r.setSubRelType("dedupSimilarity");
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r.setRelClass("isSimilarTo");
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r.setDataInfo(new DataInfo());
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switch(entity){
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case "result":
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r.setRelType("resultResult");
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break;
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case "organization":
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r.setRelType("organizationOrganization");
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break;
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default:
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throw new IllegalArgumentException("unmanaged entity type: " + entity);
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}
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return r;
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}
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}
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