116 lines
4.0 KiB
Java
116 lines
4.0 KiB
Java
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package eu.dnetlib.dhp.oa.dedup;
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import java.io.IOException;
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import java.util.Optional;
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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.JavaPairRDD;
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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.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.dom4j.DocumentException;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.xml.sax.SAXException;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.dedup.model.Block;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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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 scala.Tuple2;
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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
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.toString(
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SparkCreateSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkCreateSimRels(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, SAXException {
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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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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("isLookUpUrl: '{}'", isLookUpUrl);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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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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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaPairRDD<String, MapDocument> mapDocuments = sc
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.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.repartition(numPartitions)
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.mapToPair(
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(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, Block> blocks = Deduper
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.createSortedBlocks(mapDocuments, dedupConf)
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.repartition(numPartitions);
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Dataset<Relation> simRels = spark
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.createDataset(
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Deduper
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.computeRelations(sc, blocks, dedupConf)
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.map(t -> DedupUtility.createSimRel(t._1(), t._2(), entity))
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.repartition(numPartitions)
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.rdd(),
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Encoders.bean(Relation.class));
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saveParquet(simRels, outputPath, SaveMode.Overwrite);
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}
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}
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}
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