Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop
This commit is contained in:
commit
10e08ccf45
|
@ -59,7 +59,6 @@
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|||
<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dnet-openaire-broker-common</artifactId>
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<version>[3.0.0,)</version>
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</dependency>
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|
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</dependencies>
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|
|
|
@ -0,0 +1,57 @@
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|||
|
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package eu.dnetlib.dhp.oa.dedup;
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import java.util.Objects;
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import org.apache.spark.sql.Encoder;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.expressions.Aggregator;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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public class RelationAggregator extends Aggregator<Relation, Relation, Relation> {
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private static Relation ZERO = new Relation();
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@Override
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public Relation zero() {
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return ZERO;
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}
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@Override
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public Relation reduce(Relation b, Relation a) {
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return mergeRel(b, a);
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}
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@Override
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public Relation merge(Relation b, Relation a) {
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return mergeRel(b, a);
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}
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@Override
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public Relation finish(Relation r) {
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return r;
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}
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private Relation mergeRel(Relation b, Relation a) {
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if (Objects.equals(b, ZERO)) {
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return a;
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}
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if (Objects.equals(a, ZERO)) {
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return b;
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}
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b.mergeFrom(a);
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return b;
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}
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@Override
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public Encoder<Relation> bufferEncoder() {
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return Encoders.kryo(Relation.class);
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}
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|
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@Override
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public Encoder<Relation> outputEncoder() {
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return Encoders.kryo(Relation.class);
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}
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}
|
|
@ -5,11 +5,13 @@ import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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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.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.api.java.function.PairFunction;
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import org.apache.spark.graphx.Edge;
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import org.apache.spark.rdd.RDD;
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|
@ -75,7 +77,11 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
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final String workingPath = parser.get("workingPath");
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final String isLookUpUrl = parser.get("isLookUpUrl");
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final String actionSetId = parser.get("actionSetId");
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|
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int cut = Optional
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.ofNullable(parser.get("cutConnectedComponent"))
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.map(Integer::valueOf)
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.orElse(0);
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log.info("connected component cut: '{}'", cut);
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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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|
@ -100,8 +106,10 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
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|
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final RDD<Edge<String>> edgeRdd = spark
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.read()
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.load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity))
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.as(Encoders.bean(Relation.class))
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.textFile(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity))
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.map(
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(MapFunction<String, Relation>) r -> OBJECT_MAPPER.readValue(r, Relation.class),
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Encoders.bean(Relation.class))
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.javaRDD()
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.map(it -> new Edge<>(hash(it.getSource()), hash(it.getTarget()), it.getRelClass()))
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.rdd();
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|
@ -109,7 +117,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
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final Dataset<Relation> mergeRels = spark
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.createDataset(
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GraphProcessor
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.findCCs(vertexes.rdd(), edgeRdd, maxIterations)
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.findCCs(vertexes.rdd(), edgeRdd, maxIterations, cut)
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.toJavaRDD()
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.filter(k -> k.getDocIds().size() > 1)
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.flatMap(cc -> ccToMergeRel(cc, dedupConf))
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|
@ -117,6 +125,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
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Encoders.bean(Relation.class));
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mergeRels.write().mode(SaveMode.Append).parquet(mergeRelPath);
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}
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}
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|
|
|
@ -2,6 +2,7 @@
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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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|
@ -34,6 +35,8 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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|||
|
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private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
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public static final int NUM_PARTITIONS = 1000;
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public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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|
@ -48,13 +51,6 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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parser.parseArgument(args);
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|
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf
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.registerKryoClasses(
|
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new Class[] {
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MapDocument.class, FieldListImpl.class, FieldValueImpl.class, Block.class
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});
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new SparkCreateSimRels(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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|
@ -68,7 +64,12 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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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
|
||||
.ofNullable(parser.get("numPartitions"))
|
||||
.map(Integer::valueOf)
|
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.orElse(NUM_PARTITIONS);
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|
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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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|
@ -88,6 +89,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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|||
|
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JavaPairRDD<String, MapDocument> mapDocuments = sc
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.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.repartition(numPartitions)
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.mapToPair(
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(PairFunction<String, String, MapDocument>) s -> {
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MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
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|
@ -95,19 +97,17 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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|||
});
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|
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// create blocks for deduplication
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JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf);
|
||||
JavaPairRDD<String, Block> blocks = Deduper
|
||||
.createSortedBlocks(mapDocuments, dedupConf)
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.repartition(numPartitions);
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|
||||
// create relations by comparing only elements in the same group
|
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JavaRDD<Relation> relations = Deduper
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Deduper
|
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.computeRelations(sc, blocks, dedupConf)
|
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.map(t -> createSimRel(t._1(), t._2(), entity));
|
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|
||||
// save the simrel in the workingdir
|
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spark
|
||||
.createDataset(relations.rdd(), Encoders.bean(Relation.class))
|
||||
.write()
|
||||
.mode(SaveMode.Append)
|
||||
.save(outputPath);
|
||||
.map(t -> createSimRel(t._1(), t._2(), entity))
|
||||
.repartition(numPartitions)
|
||||
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath);
|
||||
}
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||||
}
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||||
|
||||
|
|
|
@ -4,12 +4,16 @@ package eu.dnetlib.dhp.oa.dedup;
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|||
import static org.apache.spark.sql.functions.col;
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|
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import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
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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.slf4j.Logger;
|
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import org.slf4j.LoggerFactory;
|
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|
||||
import com.google.common.base.Joiner;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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|
@ -95,7 +99,24 @@ public class SparkPropagateRelation extends AbstractSparkAction {
|
|||
FieldType.TARGET,
|
||||
getDeletedFn());
|
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|
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save(newRels.union(updated).union(mergeRels), outputRelationPath, SaveMode.Overwrite);
|
||||
save(
|
||||
distinctRelations(
|
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newRels
|
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.union(updated)
|
||||
.union(mergeRels)
|
||||
.map((MapFunction<Relation, Relation>) r -> r, Encoders.kryo(Relation.class))),
|
||||
outputRelationPath, SaveMode.Overwrite);
|
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}
|
||||
|
||||
private Dataset<Relation> distinctRelations(Dataset<Relation> rels) {
|
||||
return rels
|
||||
.filter(getRelationFilterFunction())
|
||||
.groupByKey(
|
||||
(MapFunction<Relation, String>) r -> String
|
||||
.join(r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()),
|
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Encoders.STRING())
|
||||
.agg(new RelationAggregator().toColumn())
|
||||
.map((MapFunction<Tuple2<String, Relation>, Relation>) t -> t._2(), Encoders.bean(Relation.class));
|
||||
}
|
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|
||||
private static Dataset<Relation> processDataset(
|
||||
|
@ -112,6 +133,14 @@ public class SparkPropagateRelation extends AbstractSparkAction {
|
|||
.map(mapFn, Encoders.bean(Relation.class));
|
||||
}
|
||||
|
||||
private FilterFunction<Relation> getRelationFilterFunction() {
|
||||
return (FilterFunction<Relation>) r -> StringUtils.isNotBlank(r.getSource()) ||
|
||||
StringUtils.isNotBlank(r.getTarget()) ||
|
||||
StringUtils.isNotBlank(r.getRelClass()) ||
|
||||
StringUtils.isNotBlank(r.getSubRelType()) ||
|
||||
StringUtils.isNotBlank(r.getRelClass());
|
||||
}
|
||||
|
||||
private static MapFunction<String, Relation> patchRelFn() {
|
||||
return value -> {
|
||||
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
|
||||
|
|
|
@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.dedup.graph;
|
|||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.lang.StringUtils;
|
||||
import org.codehaus.jackson.annotate.JsonIgnore;
|
||||
|
@ -18,12 +19,17 @@ public class ConnectedComponent implements Serializable {
|
|||
private Set<String> docIds;
|
||||
private String ccId;
|
||||
|
||||
public ConnectedComponent() {
|
||||
}
|
||||
|
||||
public ConnectedComponent(Set<String> docIds) {
|
||||
public ConnectedComponent(Set<String> docIds, final int cut) {
|
||||
this.docIds = docIds;
|
||||
createID();
|
||||
if (cut > 0 && docIds.size() > cut) {
|
||||
this.docIds = docIds
|
||||
.stream()
|
||||
.filter(s -> !ccId.equalsIgnoreCase(s))
|
||||
.limit(cut - 1)
|
||||
.collect(Collectors.toSet());
|
||||
this.docIds.add(ccId);
|
||||
}
|
||||
}
|
||||
|
||||
public String createID() {
|
||||
|
@ -41,6 +47,7 @@ public class ConnectedComponent implements Serializable {
|
|||
public String getMin() {
|
||||
|
||||
final StringBuilder min = new StringBuilder();
|
||||
|
||||
docIds
|
||||
.forEach(
|
||||
i -> {
|
||||
|
|
|
@ -7,7 +7,7 @@ import scala.collection.JavaConversions;
|
|||
|
||||
object GraphProcessor {
|
||||
|
||||
def findCCs(vertexes: RDD[(VertexId, String)], edges: RDD[Edge[String]], maxIterations: Int): RDD[ConnectedComponent] = {
|
||||
def findCCs(vertexes: RDD[(VertexId, String)], edges: RDD[Edge[String]], maxIterations: Int, cut:Int): RDD[ConnectedComponent] = {
|
||||
val graph: Graph[String, String] = Graph(vertexes, edges).partitionBy(PartitionStrategy.RandomVertexCut) //TODO remember to remove partitionby
|
||||
val cc = graph.connectedComponents(maxIterations).vertices
|
||||
|
||||
|
@ -22,15 +22,15 @@ object GraphProcessor {
|
|||
}
|
||||
}
|
||||
val connectedComponents = joinResult.groupByKey()
|
||||
.map[ConnectedComponent](cc => asConnectedComponent(cc))
|
||||
.map[ConnectedComponent](cc => asConnectedComponent(cc, cut))
|
||||
connectedComponents
|
||||
}
|
||||
|
||||
|
||||
|
||||
def asConnectedComponent(group: (VertexId, Iterable[String])): ConnectedComponent = {
|
||||
def asConnectedComponent(group: (VertexId, Iterable[String]), cut:Int): ConnectedComponent = {
|
||||
val docs = group._2.toSet[String]
|
||||
val connectedComponent = new ConnectedComponent(JavaConversions.setAsJavaSet[String](docs));
|
||||
val connectedComponent = new ConnectedComponent(JavaConversions.setAsJavaSet[String](docs), cut);
|
||||
connectedComponent
|
||||
}
|
||||
|
||||
|
|
|
@ -17,6 +17,12 @@
|
|||
"paramDescription": "the url for the lookup service",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "cc",
|
||||
"paramLongName": "cutConnectedComponent",
|
||||
"paramDescription": "the number of maximum elements that belongs to a connected components",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "w",
|
||||
"paramLongName": "workingPath",
|
||||
|
|
|
@ -22,5 +22,11 @@
|
|||
"paramLongName": "workingPath",
|
||||
"paramDescription": "path of the working directory",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "np",
|
||||
"paramLongName": "numPartitions",
|
||||
"paramDescription": "number of partitions for the similarity relations intermediate phases",
|
||||
"paramRequired": false
|
||||
}
|
||||
]
|
|
@ -20,6 +20,10 @@
|
|||
<name>dedupGraphPath</name>
|
||||
<description>path for the output graph</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>cutConnectedComponent</name>
|
||||
<description>max number of elements in a connected component</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
|
@ -106,10 +110,11 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--i</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--la</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--asi</arg><arg>${actionSetId}</arg>
|
||||
<arg>--w</arg><arg>${workingPath}</arg>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--numPartitions</arg><arg>8000</arg>
|
||||
</spark>
|
||||
<ok to="CreateMergeRel"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -132,10 +137,11 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--i</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--w</arg><arg>${workingPath}</arg>
|
||||
<arg>--la</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--asi</arg><arg>${actionSetId}</arg>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
|
||||
</spark>
|
||||
<ok to="CreateDedupRecord"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -158,10 +164,10 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--i</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--w</arg><arg>${workingPath}</arg>
|
||||
<arg>--la</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--asi</arg><arg>${actionSetId}</arg>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
</spark>
|
||||
<ok to="UpdateEntity"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -184,9 +190,9 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--i</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--w</arg><arg>${workingPath}</arg>
|
||||
<arg>--o</arg><arg>${dedupGraphPath}</arg>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--dedupGraphPath</arg><arg>${dedupGraphPath}</arg>
|
||||
</spark>
|
||||
<ok to="copyRelations"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
@ -3,6 +3,8 @@ package eu.dnetlib.dhp.oa.dedup;
|
|||
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
|
||||
import static org.apache.spark.sql.functions.col;
|
||||
import static org.apache.spark.sql.functions.count;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
|
@ -11,6 +13,9 @@ import java.io.IOException;
|
|||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Paths;
|
||||
import java.util.HashSet;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
|
@ -18,6 +23,7 @@ import org.apache.spark.SparkConf;
|
|||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.PairFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
|
@ -71,11 +77,13 @@ public class SparkDedupTest implements Serializable {
|
|||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
|
||||
final SparkConf conf = new SparkConf();
|
||||
conf.set("spark.sql.shuffle.partitions", "200");
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(SparkDedupTest.class.getSimpleName())
|
||||
.master("local[*]")
|
||||
.config(new SparkConf())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
|
||||
jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
@ -152,37 +160,42 @@ public class SparkDedupTest implements Serializable {
|
|||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i",
|
||||
testGraphBasePath,
|
||||
"-asi",
|
||||
testActionSetId,
|
||||
"-la",
|
||||
"lookupurl",
|
||||
"-w",
|
||||
testOutputBasePath
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-la", "lookupurl",
|
||||
"-w", testOutputBasePath,
|
||||
"-np", "50"
|
||||
});
|
||||
|
||||
new SparkCreateSimRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_simrel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
|
||||
.count();
|
||||
|
||||
long pubs_simrel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
|
||||
.count();
|
||||
long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count();
|
||||
|
||||
long ds_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/dataset_simrel").count();
|
||||
long sw_simrel = spark
|
||||
.read()
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/software_simrel")
|
||||
.count();
|
||||
|
||||
long ds_simrel = spark
|
||||
.read()
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_simrel")
|
||||
.count();
|
||||
|
||||
long orp_simrel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_simrel")
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_simrel")
|
||||
.count();
|
||||
|
||||
assertEquals(3432, orgs_simrel);
|
||||
assertEquals(7054, pubs_simrel);
|
||||
assertEquals(7152, pubs_simrel);
|
||||
assertEquals(344, sw_simrel);
|
||||
assertEquals(458, ds_simrel);
|
||||
assertEquals(6750, orp_simrel);
|
||||
|
@ -190,6 +203,101 @@ public class SparkDedupTest implements Serializable {
|
|||
|
||||
@Test
|
||||
@Order(2)
|
||||
public void cutMergeRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateMergeRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i",
|
||||
testGraphBasePath,
|
||||
"-asi",
|
||||
testActionSetId,
|
||||
"-la",
|
||||
"lookupurl",
|
||||
"-w",
|
||||
testOutputBasePath,
|
||||
"-cc",
|
||||
"3"
|
||||
});
|
||||
|
||||
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_mergerel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
|
||||
.groupBy("source")
|
||||
.agg(count("target").alias("cnt"))
|
||||
.select("source", "cnt")
|
||||
.where("cnt > 3")
|
||||
.count();
|
||||
|
||||
long pubs_mergerel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
|
||||
.groupBy("source")
|
||||
.agg(count("target").alias("cnt"))
|
||||
.select("source", "cnt")
|
||||
.where("cnt > 3")
|
||||
.count();
|
||||
long sw_mergerel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
|
||||
.groupBy("source")
|
||||
.agg(count("target").alias("cnt"))
|
||||
.select("source", "cnt")
|
||||
.where("cnt > 3")
|
||||
.count();
|
||||
|
||||
long ds_mergerel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
|
||||
.groupBy("source")
|
||||
.agg(count("target").alias("cnt"))
|
||||
.select("source", "cnt")
|
||||
.where("cnt > 3")
|
||||
.count();
|
||||
|
||||
long orp_mergerel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
|
||||
.groupBy("source")
|
||||
.agg(count("target").alias("cnt"))
|
||||
.select("source", "cnt")
|
||||
.where("cnt > 3")
|
||||
.count();
|
||||
|
||||
assertEquals(0, orgs_mergerel);
|
||||
assertEquals(0, pubs_mergerel);
|
||||
assertEquals(0, sw_mergerel);
|
||||
assertEquals(0, ds_mergerel);
|
||||
assertEquals(0, orp_mergerel);
|
||||
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel"));
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel"));
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/software_mergerel"));
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel"));
|
||||
FileUtils
|
||||
.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel"));
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(3)
|
||||
public void createMergeRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
|
@ -225,8 +333,10 @@ public class SparkDedupTest implements Serializable {
|
|||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
|
||||
.count();
|
||||
|
||||
long ds_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel").count();
|
||||
long ds_mergerel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
|
||||
.count();
|
||||
|
||||
long orp_mergerel = spark
|
||||
.read()
|
||||
|
@ -234,14 +344,14 @@ public class SparkDedupTest implements Serializable {
|
|||
.count();
|
||||
|
||||
assertEquals(1276, orgs_mergerel);
|
||||
assertEquals(1440, pubs_mergerel);
|
||||
assertEquals(1442, pubs_mergerel);
|
||||
assertEquals(288, sw_mergerel);
|
||||
assertEquals(472, ds_mergerel);
|
||||
assertEquals(718, orp_mergerel);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(3)
|
||||
@Order(4)
|
||||
public void createDedupRecordTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
|
@ -288,7 +398,7 @@ public class SparkDedupTest implements Serializable {
|
|||
}
|
||||
|
||||
@Test
|
||||
@Order(4)
|
||||
@Order(5)
|
||||
public void updateEntityTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
|
@ -404,7 +514,7 @@ public class SparkDedupTest implements Serializable {
|
|||
}
|
||||
|
||||
@Test
|
||||
@Order(5)
|
||||
@Order(6)
|
||||
public void propagateRelationTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
|
@ -423,7 +533,7 @@ public class SparkDedupTest implements Serializable {
|
|||
|
||||
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
||||
|
||||
assertEquals(4971, relations);
|
||||
assertEquals(4866, relations);
|
||||
|
||||
// check deletedbyinference
|
||||
final Dataset<Relation> mergeRels = spark
|
||||
|
@ -454,7 +564,7 @@ public class SparkDedupTest implements Serializable {
|
|||
}
|
||||
|
||||
@Test
|
||||
@Order(6)
|
||||
@Order(7)
|
||||
public void testRelations() throws Exception {
|
||||
testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10);
|
||||
testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2);
|
||||
|
|
|
@ -6,10 +6,10 @@
|
|||
"subEntityType" : "resulttype",
|
||||
"subEntityValue" : "dataset",
|
||||
"orderField" : "title",
|
||||
"queueMaxSize" : "800",
|
||||
"queueMaxSize" : "100",
|
||||
"groupMaxSize" : "100",
|
||||
"maxChildren" : "100",
|
||||
"slidingWindowSize" : "80",
|
||||
"slidingWindowSize" : "100",
|
||||
"rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
|
||||
"includeChildren" : "true",
|
||||
"idPath" : "$.id",
|
||||
|
@ -17,7 +17,8 @@
|
|||
},
|
||||
"pace" : {
|
||||
"clustering" : [
|
||||
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
|
||||
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
|
||||
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
|
||||
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
|
||||
],
|
||||
"decisionTree" : {
|
||||
|
|
|
@ -6,10 +6,10 @@
|
|||
"subEntityType" : "resulttype",
|
||||
"subEntityValue" : "otherresearchproduct",
|
||||
"orderField" : "title",
|
||||
"queueMaxSize" : "800",
|
||||
"queueMaxSize" : "100",
|
||||
"groupMaxSize" : "100",
|
||||
"maxChildren" : "100",
|
||||
"slidingWindowSize" : "80",
|
||||
"slidingWindowSize" : "100",
|
||||
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
|
||||
"includeChildren" : "true",
|
||||
"idPath" : "$.id",
|
||||
|
@ -17,7 +17,8 @@
|
|||
},
|
||||
"pace" : {
|
||||
"clustering" : [
|
||||
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
|
||||
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
|
||||
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
|
||||
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
|
||||
],
|
||||
"decisionTree" : {
|
||||
|
|
|
@ -6,10 +6,10 @@
|
|||
"subEntityType": "resulttype",
|
||||
"subEntityValue": "publication",
|
||||
"orderField": "title",
|
||||
"queueMaxSize": "800",
|
||||
"queueMaxSize": "100",
|
||||
"groupMaxSize": "100",
|
||||
"maxChildren": "100",
|
||||
"slidingWindowSize": "80",
|
||||
"slidingWindowSize": "100",
|
||||
"rootBuilder": [
|
||||
"result",
|
||||
"resultProject_outcome_isProducedBy",
|
||||
|
@ -29,7 +29,8 @@
|
|||
},
|
||||
"pace": {
|
||||
"clustering" : [
|
||||
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
|
||||
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
|
||||
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
|
||||
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
|
||||
],
|
||||
"decisionTree": {
|
||||
|
|
|
@ -6,10 +6,10 @@
|
|||
"subEntityType" : "resulttype",
|
||||
"subEntityValue" : "software",
|
||||
"orderField" : "title",
|
||||
"queueMaxSize" : "800",
|
||||
"queueMaxSize" : "100",
|
||||
"groupMaxSize" : "100",
|
||||
"maxChildren" : "100",
|
||||
"slidingWindowSize" : "80",
|
||||
"slidingWindowSize" : "100",
|
||||
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
|
||||
"includeChildren" : "true",
|
||||
"idPath" : "$.id",
|
||||
|
@ -17,8 +17,9 @@
|
|||
},
|
||||
"pace" : {
|
||||
"clustering" : [
|
||||
{ "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
|
||||
{ "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } }
|
||||
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
|
||||
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
|
||||
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
|
||||
],
|
||||
"decisionTree": {
|
||||
"start": {
|
||||
|
|
7
pom.xml
7
pom.xml
|
@ -323,6 +323,12 @@
|
|||
<version>[2.0.0,3.0.0)</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>eu.dnetlib.dhp</groupId>
|
||||
<artifactId>dnet-openaire-broker-common</artifactId>
|
||||
<version>${dnet.openaire.broker.common}</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.cxf</groupId>
|
||||
<artifactId>cxf-rt-transports-http</artifactId>
|
||||
|
@ -618,5 +624,6 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dnet.openaire.broker.common>3.0.0</dnet.openaire.broker.common>
|
||||
</properties>
|
||||
</project>
|
||||
|
|
Loading…
Reference in New Issue