126 lines
4.2 KiB
Java
126 lines
4.2 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 eu.dnetlib.dhp.schema.oaf.Relation;
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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.MapFunction;
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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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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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 scala.Tuple2;
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public class SparkCreateOrgsDedupRecord extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCreateOrgsDedupRecord.class);
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public SparkCreateOrgsDedupRecord(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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SparkCreateOrgsDedupRecord.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgs_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkCreateOrgsDedupRecord(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 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("Copying organization dedup records to the working dir");
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final String outputPath = DedupUtility.createDedupRecordPath(workingPath, actionSetId, "organization");
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final String entityPath = DedupUtility.createEntityPath(graphBasePath, "organization");
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final String mergeRelsPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, "organization");
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rootOrganization(spark, entityPath, mergeRelsPath)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
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}
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public static Dataset<Organization> rootOrganization(
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final SparkSession spark,
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final String entitiesInputPath,
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final String mergeRelsPath) {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaPairRDD<String, Organization> entities = sc.textFile(entitiesInputPath)
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.map(it -> OBJECT_MAPPER.readValue(it, Organization.class))
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.mapToPair(o -> new Tuple2<>(o.getId(), o));
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log.info("Number of organization entities processed: {}", entities.count());
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//collect root ids (ids in the source of 'merges' relations
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JavaPairRDD<String, String> roots = spark
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.read()
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.load(mergeRelsPath)
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.as(Encoders.bean(Relation.class))
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.where("relClass == 'merges'")
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.map(
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(MapFunction<Relation, Tuple2<String, String>>) r -> new Tuple2<>(r.getSource(), "root"),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
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.toJavaRDD()
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.mapToPair(t -> t)
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.distinct();
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Dataset<Organization> rootOrgs = spark.createDataset(
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entities
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.leftOuterJoin(roots)
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.filter(e -> e._2()._2().isPresent()) //if it has been joined with 'root' then it's a root record
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.map(e -> e._2()._1())
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.rdd(),
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Encoders.bean(Organization.class));
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log.info("Number of Root organization: {}", entities.count());
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return rootOrgs;
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}
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}
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