forked from D-Net/dnet-hadoop
116 lines
5.0 KiB
Java
116 lines
5.0 KiB
Java
package eu.dnetlib.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.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset;
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import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication;
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import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown;
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import eu.dnetlib.dhp.utils.DHPUtils;
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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.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 scala.Tuple2;
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import java.io.IOException;
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public class SparkUpdateEntityJob {
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final static String IDJSONPATH = "$.id";
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final static String SOURCEJSONPATH = "$.source";
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final static String TARGETJSONPATH = "$.target";
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkUpdateEntityJob.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/dedup_delete_by_inference_parameters.json")));
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parser.parseArgument(args);
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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkUpdateEntityJob.class.getSimpleName())
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.master(parser.get("master"))
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.getOrCreate();
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final String entityPath = parser.get("entityPath");
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final String mergeRelPath = parser.get("mergeRelPath");
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final String dedupRecordPath = parser.get("dedupRecordPath");
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final String entity = parser.get("entity");
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final String destination = parser.get("targetPath");
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final Dataset<Relation> df = spark.read().load(mergeRelPath).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(entityPath);
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if ("relation".equalsIgnoreCase(entity)) {
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sourceEntity.mapToPair(
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(PairFunction<String, String, String>) s ->
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new Tuple2<>(DHPUtils.getJPathString(SOURCEJSONPATH, s), s))
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.leftOuterJoin(mergedIds)
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.map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), Relation.class) : k._2()._1())
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.mapToPair((PairFunction<String, String, String>) s -> new Tuple2<>(DHPUtils.getJPathString(TARGETJSONPATH, s), s))
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.leftOuterJoin(mergedIds)
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.map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), Relation.class) : k._2()._1())
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.saveAsTextFile(destination, GzipCodec.class);
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} else {
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final JavaRDD<String> dedupEntity = sc.textFile(dedupRecordPath);
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JavaPairRDD<String, String> entitiesWithId = sourceEntity.mapToPair((PairFunction<String, String, String>) s -> new Tuple2<>(DHPUtils.getJPathString(IDJSONPATH, s), s));
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Class<? extends Oaf> mainClass;
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switch (entity) {
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case "publication":
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mainClass = DLIPublication.class;
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break;
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case "dataset":
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mainClass = DLIDataset.class;
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break;
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case "unknown":
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mainClass = DLIUnknown.class;
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break;
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default:
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throw new IllegalArgumentException("Illegal type " + entity);
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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(destination, GzipCodec.class);
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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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}
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