forked from D-Net/dnet-hadoop
123 lines
4.1 KiB
Java
123 lines
4.1 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.Collection;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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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.JavaSparkContext;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.catalyst.expressions.Literal;
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import org.apache.spark.sql.types.DataTypes;
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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.BlockStats;
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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.RowDataOrderingComparator;
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import eu.dnetlib.pace.model.SparkDedupConfig;
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public class SparkBlockStats extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkBlockStats.class);
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public SparkBlockStats(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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SparkBlockStats.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/createBlockStats_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkBlockStats(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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public Long computeComparisons(Long blockSize, Long slidingWindowSize) {
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if (slidingWindowSize >= blockSize)
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return (slidingWindowSize * (slidingWindowSize - 1)) / 2;
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else {
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return (blockSize - slidingWindowSize + 1) * (slidingWindowSize * (slidingWindowSize - 1)) / 2;
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}
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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("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 subEntity = dedupConf.getWf().getSubEntityValue();
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log.info("Creating blockstats for: '{}'", subEntity);
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final String outputPath = DedupUtility.createBlockStatsPath(workingPath, actionSetId, subEntity);
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removeOutputDir(spark, outputPath);
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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SparkDedupConfig sparkConfig = new SparkDedupConfig(dedupConf, numPartitions);
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Dataset<Row> inputDF = spark
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.read()
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.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.transform(sparkConfig.modelExtractor());
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Dataset<Row> simRels = inputDF
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.transform(sparkConfig.generateClusters())
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.filter(functions.size(new Column("block")).geq(new Literal(1, DataTypes.IntegerType)));
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simRels.map(b -> {
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Collection<Row> documents = b.getList(1);
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List<Row> mapDocuments = documents
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.stream()
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.sorted(new RowDataOrderingComparator(sparkConfig.orderingFieldPosition()))
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.limit(dedupConf.getWf().getQueueMaxSize())
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.collect(Collectors.toList());
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return new BlockStats(
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b.getString(0),
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(long) mapDocuments.size(),
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computeComparisons(
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(long) mapDocuments.size(), (long) dedupConf.getWf().getSlidingWindowSize()));
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}, Encoders.bean(BlockStats.class))
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.write()
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.mode(SaveMode.Overwrite)
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.save(outputPath);
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}
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}
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}
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