forked from D-Net/dnet-hadoop
116 lines
4.1 KiB
Java
116 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.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.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.*;
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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.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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public class SparkWhitelistSimRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkWhitelistSimRels.class);
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private static final String WHITELIST_SEPARATOR = "####";
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public SparkWhitelistSimRels(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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SparkWhitelistSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkWhitelistSimRels(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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final String whiteListPath = parser.get("whiteListPath");
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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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log.info("whiteListPath: '{}'", whiteListPath);
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// file format: source####target
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Dataset<Row> whiteListRels = spark
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.read()
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.textFile(whiteListPath)
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.withColumn("pairs", functions.split(new Column("value"), WHITELIST_SEPARATOR))
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.filter(functions.size(new Column("pairs")).equalTo(2))
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.select(
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functions.element_at(new Column("pairs"), 1).as("from"),
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functions.element_at(new Column("pairs"), 2).as("to"));
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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("Adding whitelist simrels for: '{}'", subEntity);
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final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
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// DFMapDocumentUtils.registerUDFs(spark, dedupConf);
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Dataset<Row> entities = spark
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.read()
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.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.repartition(numPartitions)
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.withColumn("id", functions.get_json_object(new Column("value"), dedupConf.getWf().getIdPath()));
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Dataset<Row> whiteListRels1 = whiteListRels
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.join(entities, entities.col("id").equalTo(whiteListRels.col("from")), "inner")
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.select("from", "to");
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Dataset<Row> whiteListRels2 = whiteListRels1
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.join(entities, whiteListRels1.col("to").equalTo(entities.col("id")), "inner")
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.select("from", "to");
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Dataset<Relation> whiteListSimRels = whiteListRels2
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.map(
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(MapFunction<Row, Relation>) r -> DedupUtility
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.createSimRel(r.getString(0), r.getString(1), entity),
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Encoders.bean(Relation.class));
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saveParquet(whiteListSimRels, outputPath, SaveMode.Append);
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}
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}
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}
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