116 lines
4.4 KiB
Java
116 lines
4.4 KiB
Java
package eu.dnetlib.dhp.oa.dedup;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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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 org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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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 java.io.IOException;
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import java.util.Optional;
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//copy simrels (verified) from relation to the workdir in order to make them available for the deduplication
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public class SparkCopyRels extends AbstractSparkAction{
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private static final Logger log = LoggerFactory.getLogger(SparkCopyRels.class);
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public SparkCopyRels(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
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.toString(
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SparkCopyRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyRels_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkCopyRels(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@Override
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public void run(ISLookUpService isLookUpService)
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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 actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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final String destination = parser.get("destination");
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final String entity = parser.get("entityType");
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final int numPartitions = Optional
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.ofNullable(parser.get("numPartitions"))
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.map(Integer::valueOf)
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.orElse(NUM_PARTITIONS);
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log.info("numPartitions: '{}'", numPartitions);
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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log.info("entity: '{}'", entity);
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log.info("Copying " + destination + " for: '{}'", entity);
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final String outputPath;
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if (destination.contains("mergerel")) {
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outputPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, entity);
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}
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else {
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outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, entity);
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}
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removeOutputDir(spark, outputPath);
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
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JavaRDD<Relation> simRels =
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spark.read()
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.textFile(relationPath)
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.map(patchRelFn(), Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(r -> filterRels(r, entity));
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simRels.saveAsTextFile(outputPath);
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}
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private static MapFunction<String, Relation> patchRelFn() {
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return value -> {
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final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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return rel;
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};
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}
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private boolean filterRels(Relation rel, String entityType) {
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switch(entityType) {
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case "result":
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if (rel.getRelClass().equals("isSimilarTo") && rel.getRelType().equals("resultResult") && rel.getSubRelType().equals("dedup"))
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return true;
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break;
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case "organization":
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if (rel.getRelClass().equals("isSimilarTo") && rel.getRelType().equals("organizationOrganization") && rel.getSubRelType().equals("dedup"))
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return true;
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break;
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default:
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return false;
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}
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return false;
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}
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}
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