forked from D-Net/dnet-hadoop
122 lines
5.3 KiB
Java
122 lines
5.3 KiB
Java
package eu.dnetlib.dhp.dedup;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.pace.config.DedupConfig;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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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.JavaRDD;
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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.Row;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.DocumentException;
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import scala.Tuple2;
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import java.io.IOException;
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public class SparkUpdateEntity {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/updateEntity_parameters.json")));
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parser.parseArgument(args);
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new SparkUpdateEntity().run(parser);
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}
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public void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException {
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final String graphBasePath = parser.get("graphBasePath");
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final String workingPath = parser.get("workingPath");
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final String dedupGraphPath = parser.get("dedupGraphPath");
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final String isLookUpUrl = parser.get("isLookUpUrl");
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final String actionSetId = parser.get("actionSetId");
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try (SparkSession spark = getSparkSession(parser)) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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for (DedupConfig dedupConf : DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) {
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String subEntity = dedupConf.getWf().getSubEntityValue();
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final Dataset<Relation> df = spark.read().load(DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class));
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final JavaPairRDD<String, String> mergedIds = df
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.where("relClass == 'merges'")
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.select(df.col("target"))
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.distinct()
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.toJavaRDD()
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.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
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final JavaRDD<String> sourceEntity = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity));
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final JavaRDD<String> dedupEntity = sc.textFile(DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity));
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JavaPairRDD<String, String> entitiesWithId = sourceEntity.mapToPair((PairFunction<String, String, String>) s -> new Tuple2<>(MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s), s));
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Class<? extends Oaf> mainClass;
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switch (subEntity) {
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case "publication":
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mainClass = Publication.class;
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break;
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case "dataset":
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mainClass = eu.dnetlib.dhp.schema.oaf.Dataset.class;
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break;
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case "datasource":
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mainClass = Datasource.class;
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break;
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case "software":
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mainClass = Software.class;
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break;
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case "organization":
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mainClass = Organization.class;
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break;
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case "otherresearchproduct":
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mainClass = OtherResearchProduct.class;
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break;
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default:
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throw new IllegalArgumentException("Illegal type " + subEntity);
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}
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JavaRDD<String> map = entitiesWithId.leftOuterJoin(mergedIds).map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), mainClass) : k._2()._1());
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map.union(dedupEntity).saveAsTextFile(dedupGraphPath + "/" + subEntity, GzipCodec.class);
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}
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}
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}
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private static <T extends Oaf> String updateDeletedByInference(final String json, final Class<T> clazz) {
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final ObjectMapper mapper = new ObjectMapper();
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mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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try {
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Oaf entity = mapper.readValue(json, clazz);
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if (entity.getDataInfo()== null)
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entity.setDataInfo(new DataInfo());
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entity.getDataInfo().setDeletedbyinference(true);
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return mapper.writeValueAsString(entity);
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} catch (IOException e) {
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throw new RuntimeException("Unable to convert json", e);
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}
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}
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private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
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SparkConf conf = new SparkConf();
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return SparkSession
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.builder()
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.appName(SparkUpdateEntity.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.enableHiveSupport()
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.getOrCreate();
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}
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}
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