104 lines
4.8 KiB
Java
104 lines
4.8 KiB
Java
package eu.dnetlib;
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import com.google.common.collect.Iterables;
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import eu.dnetlib.graph.GraphProcessor;
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import eu.dnetlib.pace.config.DedupConfig;
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import eu.dnetlib.pace.model.MapDocument;
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import eu.dnetlib.pace.utils.PaceUtils;
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import eu.dnetlib.reporter.SparkBlockProcessor;
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import eu.dnetlib.reporter.SparkReporter;
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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.graphx.Edge;
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import org.apache.spark.rdd.RDD;
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import org.apache.spark.sql.SparkSession;
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import org.apache.spark.util.LongAccumulator;
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import scala.Tuple2;
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import java.net.URL;
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import java.util.Map;
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import java.util.stream.Collectors;
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public class SparkLocalTest {
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public static void main(String[] args) {
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final SparkSession spark = SparkSession
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.builder()
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.appName("Deduplication")
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.master("local[*]")
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.getOrCreate();
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final JavaSparkContext context = new JavaSparkContext(spark.sparkContext());
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final URL dataset = SparkLocalTest.class.getResource("/eu/dnetlib/pace/organization.to.fix.json");
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final JavaRDD<String> dataRDD = context.textFile(dataset.getPath());
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//read the configuration from the classpath
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final DedupConfig config = DedupConfig.load(Utility.readFromClasspath("/eu/dnetlib/pace/org.curr.conf", SparkLocalTest.class));
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Map<String, LongAccumulator> accumulators = Utility.constructAccumulator(config, context.sc());
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//create vertexes of the graph: <ID, MapDocument>
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JavaPairRDD<String, MapDocument> mapDocs = dataRDD.mapToPair(it -> {
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MapDocument mapDocument = PaceUtils.asMapDocument(config, it);
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return new Tuple2<>(mapDocument.getIdentifier(), mapDocument);
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});
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// mapDocs.filter(d -> d._2().getFieldMap().get("doi").stringValue().length() > 0).foreach(d -> System.out.println(d));
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// mapDocs.filter(d -> d._2().getFieldMap().get("documentationUrl").stringValue().length() > 0).foreach(d -> System.out.println(d));
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RDD<Tuple2<Object, MapDocument>> vertexes = mapDocs.mapToPair(t -> new Tuple2<Object, MapDocument>( (long) t._1().hashCode(), t._2())).rdd();
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//create relations between documents
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JavaPairRDD<String, Iterable<MapDocument>> blocks = mapDocs.reduceByKey((a, b) -> a) //the reduce is just to be sure that we haven't document with same id
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//Clustering: from <id, doc> to List<groupkey,doc>
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.flatMapToPair(a -> {
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final MapDocument currentDocument = a._2();
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return Utility.getGroupingKeys(config, currentDocument).stream()
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.map(it -> new Tuple2<>(it, currentDocument)).collect(Collectors.toList()).iterator();
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}).groupByKey();//group documents basing on the key
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//print blocks
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// blocks = blocks.filter(b -> Iterables.size(b._2())>1);
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//// vertexes = blocks.flatMap(b -> b._2().iterator()).map(t -> new Tuple2<Object, MapDocument>((long) t.getIdentifier().hashCode(), t)).rdd();
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// blocks.map(group -> new DocumentsBlock(group._1(), group._2())).foreach(b -> System.out.println(b));
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//create relations by comparing only elements in the same group
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final JavaPairRDD<String, String> relationRDD = blocks.flatMapToPair(it -> {
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final SparkReporter reporter = new SparkReporter();
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new SparkBlockProcessor(config).process(it._1(), it._2(), reporter, accumulators);
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return reporter.getReport().iterator();
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});
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final RDD<Edge<String>> edgeRdd = relationRDD.map(it -> new Edge<>(it._1().hashCode(),it._2().hashCode(), "similarTo")).rdd();
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JavaRDD<ConnectedComponent> ccs = GraphProcessor.findCCs(vertexes, edgeRdd, 20).toJavaRDD();
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final JavaRDD<ConnectedComponent> connectedComponents = ccs.filter(cc -> cc.getDocs().size()>1);
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final JavaRDD<ConnectedComponent> nonDeduplicated = ccs.filter(cc -> cc.getDocs().size()==1);
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//print deduped
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connectedComponents.foreach(cc -> {
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System.out.println(cc);
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});
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//print nondeduped
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nonDeduplicated.foreach(cc -> {
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System.out.println(cc);
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});
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System.out.println("Non duplicates: " + nonDeduplicated.count());
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System.out.println("Duplicates: " + connectedComponents.flatMap(cc -> cc.getDocs().iterator()).count());
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System.out.println("Connected Components: " + connectedComponents.count());
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accumulators.forEach((name, acc) -> System.out.println(name + " -> " + acc.value()));
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// //print ids
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// ccs.foreach(cc -> System.out.println(cc.getId()));
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// connectedComponents.saveAsTextFile("file:///Users/miconis/Downloads/dumps/organizations_dedup");
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}
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} |