implementation of the whitelist for similarity relations
This commit is contained in:
miconis
parent
954a16c213
commit
853333bdde
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@ -0,0 +1,151 @@
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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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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.FilterFunction;
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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.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 org.xml.sax.SAXException;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.dedup.model.Block;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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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 eu.dnetlib.pace.config.DedupConfig;
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import eu.dnetlib.pace.model.MapDocument;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import scala.Tuple2;
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import scala.Tuple3;
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public class SparkWhitelistSimRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
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private static final String WHITELIST_SEPARATOR = "####";
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public SparkWhitelistSimRels(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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SparkCreateSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkWhitelistSimRels(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, SAXException {
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// read oozie parameters
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final String graphBasePath = parser.get("graphBasePath");
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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
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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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final String whiteListPath = parser.get("whiteListPath");
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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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log.info("workingPath: '{}'", workingPath);
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log.info("whiteListPath: '{}'", whiteListPath);
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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//file format: source####target
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Dataset<Tuple2<String, String>> whiteListRels = spark.createDataset(sc
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.textFile(whiteListPath)
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//check if the line is in the correct format: id1####id2
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.filter(s -> s.contains(WHITELIST_SEPARATOR) && s.split(WHITELIST_SEPARATOR).length == 2)
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.map(s -> new Tuple2<>(s.split(WHITELIST_SEPARATOR)[0], s.split(WHITELIST_SEPARATOR)[1]))
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.rdd(),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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// for each dedup configuration
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for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
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final String entity = dedupConf.getWf().getEntityType();
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final String subEntity = dedupConf.getWf().getSubEntityValue();
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log.info("Adding whitelist simrels for: '{}'", subEntity);
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final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
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Dataset<Tuple2<String, String>> entities = spark.createDataset(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, String>) s -> {
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MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
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return new Tuple2<>(d.getIdentifier(), "present");
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})
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.rdd(),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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Dataset<Tuple2<String, String>> whiteListRels1 = whiteListRels
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.joinWith(entities, whiteListRels.col("_1").equalTo(entities.col("_1")), "inner")
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.map((MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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Dataset<Tuple2<String, String>> whiteListRels2 = whiteListRels1
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.joinWith(entities, whiteListRels1.col("_2").equalTo(entities.col("_1")), "inner")
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.map((MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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Dataset<Relation> whiteListSimRels = whiteListRels2
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.map((MapFunction<Tuple2<String, String>, Relation>)
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r -> createSimRel(r._1(), r._2(), entity),
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Encoders.bean(Relation.class)
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);
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saveParquet(whiteListSimRels, outputPath, SaveMode.Append);
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}
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}
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private Relation createSimRel(String source, String target, String entity) {
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final Relation r = new Relation();
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r.setSource(source);
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r.setTarget(target);
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r.setSubRelType("dedupSimilarity");
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r.setRelClass("isSimilarTo");
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r.setDataInfo(new DataInfo());
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switch (entity) {
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case "result":
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r.setRelType("resultResult");
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break;
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case "organization":
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r.setRelType("organizationOrganization");
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break;
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default:
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throw new IllegalArgumentException("unmanaged entity type: " + entity);
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}
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return r;
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}
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}
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@ -20,6 +20,10 @@
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<name>workingPath</name>
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<description>path for the working directory</description>
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</property>
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<property>
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<name>whiteListPath</name>
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<description>path for the whitelist of similarity relations</description>
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</property>
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<property>
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<name>dedupGraphPath</name>
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<description>path for the output graph</description>
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@ -130,6 +134,34 @@
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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<arg>--numPartitions</arg><arg>8000</arg>
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</spark>
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<ok to="WhitelistSimRels"/>
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<error to="Kill"/>
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</action>
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<action name="WhitelistSimRels">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Add Whitelist Similarity Relations</name>
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<class>eu.dnetlib.dhp.oa.dedup.SparkWhitelistSimRels</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=3840
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</spark-opts>
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<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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<arg>--actionSetId</arg><arg>${actionSetId}</arg>
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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<arg>--whiteListPath</arg><arg>${whiteListPath}</arg>
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<arg>--numPartitions</arg><arg>8000</arg>
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</spark>
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<ok to="CreateMergeRel"/>
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<error to="Kill"/>
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</action>
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@ -0,0 +1,38 @@
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[
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{
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"paramName": "la",
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"paramLongName": "isLookUpUrl",
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"paramDescription": "address for the LookUp",
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"paramRequired": true
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},
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{
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"paramName": "asi",
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"paramLongName": "actionSetId",
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"paramDescription": "action set identifier (name of the orchestrator)",
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"paramRequired": true
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},
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{
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"paramName": "i",
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"paramLongName": "graphBasePath",
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"paramDescription": "the base path of the raw graph",
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"paramRequired": true
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},
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{
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"paramName": "w",
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"paramLongName": "workingPath",
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"paramDescription": "path of the working directory",
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"paramRequired": true
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},
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{
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"paramName": "np",
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"paramLongName": "numPartitions",
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"paramDescription": "number of partitions for the similarity relations intermediate phases",
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"paramRequired": false
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},
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{
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"paramName": "wl",
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"paramLongName": "whiteListPath",
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"paramDescription": "whitelist file path for the addition of custom simrels",
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"paramRequired": true
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}
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]
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@ -5,13 +5,16 @@ import static java.nio.file.Files.createTempDirectory;
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import static org.apache.spark.sql.functions.count;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.mockito.Mockito.lenient;
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import java.io.File;
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import java.io.FileReader;
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import java.io.IOException;
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import java.io.Serializable;
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import java.net.URISyntaxException;
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import java.nio.file.Paths;
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import java.util.List;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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@ -55,6 +58,10 @@ public class SparkDedupTest implements Serializable {
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private static String testOutputBasePath;
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private static String testDedupGraphBasePath;
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private static final String testActionSetId = "test-orchestrator";
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private static String whitelistPath;
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private static List<String> whiteList;
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private static String WHITELIST_SEPARATOR = "####";
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@BeforeAll
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public static void cleanUp() throws IOException, URISyntaxException {
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@ -71,6 +78,12 @@ public class SparkDedupTest implements Serializable {
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.toAbsolutePath()
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.toString();
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whitelistPath = Paths
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.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/whitelist.simrels.txt").toURI())
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.toFile()
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.getAbsolutePath();
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whiteList = IOUtils.readLines(new FileReader(whitelistPath));
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FileUtils.deleteDirectory(new File(testOutputBasePath));
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FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
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@ -202,6 +215,78 @@ public class SparkDedupTest implements Serializable {
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@Test
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@Order(2)
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void whitelistSimRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkWhitelistSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")));
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parser
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.parseArgument(
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new String[]{
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"-i", testGraphBasePath,
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"-asi", testActionSetId,
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"-la", "lookupurl",
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"-w", testOutputBasePath,
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"-np", "50",
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"-wl", whitelistPath
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});
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new SparkWhitelistSimRels(parser, spark).run(isLookUpService);
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long orgs_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
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.count();
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long pubs_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication"))
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.count();
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long ds_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset"))
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.count();
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long orp_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct"))
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.count();
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//entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
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assertEquals(3082, orgs_simrel);
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assertEquals(7036, pubs_simrel);
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assertEquals(442, ds_simrel);
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assertEquals(6750, orp_simrel);
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//entities simrels to be different from the number of previous step (new simrels in the whitelist)
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Dataset<Row> sw_simrel = spark
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.read()
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.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software"));
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//check if the first relation in the whitelist exists
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assertTrue(sw_simrel
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.as(Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(rel ->
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rel.getSource().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[0]) && rel.getTarget().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[1])).count() > 0);
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//check if the second relation in the whitelist exists
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assertTrue(sw_simrel
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.as(Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(rel ->
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rel.getSource().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[0]) && rel.getTarget().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[1])).count() > 0);
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assertEquals(338, sw_simrel.count());
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}
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@Test
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@Order(3)
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void cutMergeRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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@ -297,7 +382,7 @@ public class SparkDedupTest implements Serializable {
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}
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@Test
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@Order(3)
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@Order(4)
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void createMergeRelsTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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@ -353,7 +438,7 @@ public class SparkDedupTest implements Serializable {
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}
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@Test
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@Order(4)
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@Order(5)
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void createDedupRecordTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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@ -394,13 +479,13 @@ public class SparkDedupTest implements Serializable {
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assertEquals(85, orgs_deduprecord);
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assertEquals(65, pubs_deduprecord);
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assertEquals(51, sw_deduprecord);
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assertEquals(49, sw_deduprecord);
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assertEquals(97, ds_deduprecord);
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assertEquals(89, orp_deduprecord);
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}
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@Test
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@Order(5)
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@Order(6)
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void updateEntityTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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@ -479,7 +564,7 @@ public class SparkDedupTest implements Serializable {
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assertEquals(838, organizations);
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assertEquals(100, projects);
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assertEquals(100, datasource);
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assertEquals(200, softwares);
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assertEquals(198, softwares);
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assertEquals(389, dataset);
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assertEquals(517, otherresearchproduct);
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@ -516,7 +601,7 @@ public class SparkDedupTest implements Serializable {
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}
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@Test
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@Order(6)
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@Order(7)
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void propagateRelationTest() throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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@ -566,7 +651,7 @@ public class SparkDedupTest implements Serializable {
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}
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@Test
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@Order(7)
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@Order(8)
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void testRelations() throws Exception {
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testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10);
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testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2);
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@ -0,0 +1,2 @@
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50|r37b0ad08687::f645b9729d1e1025a72c57883f0f2cac####50|r37b0ad08687::4c55b436743b5c49fa32cd582fd9e1aa
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50|datacite____::a90f49f9fde5393c00633bea6e4e374a####50|datacite____::5f55cdee77303ba8a2bf9996c32a330c
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