2020-03-27 10:42:17 +01:00
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package eu.dnetlib.dhp.oa.dedup;
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2019-12-06 13:38:00 +01:00
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2020-03-20 13:01:56 +01:00
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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2019-12-06 13:38:00 +01:00
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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2020-03-20 13:01:56 +01:00
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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2019-12-06 13:38:00 +01:00
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import eu.dnetlib.dhp.schema.oaf.Relation;
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2020-04-01 18:48:31 +02:00
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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2020-03-20 13:01:56 +01:00
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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2020-04-01 18:48:31 +02:00
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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2019-12-06 13:38:00 +01:00
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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 org.apache.commons.io.IOUtils;
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2020-03-20 13:01:56 +01:00
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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2019-12-06 13:38:00 +01:00
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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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2020-04-01 18:48:31 +02:00
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import org.apache.spark.api.java.function.PairFunction;
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2019-12-06 13:38:00 +01:00
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.Document;
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2020-03-20 13:01:56 +01:00
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import org.dom4j.DocumentException;
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2020-04-01 18:48:31 +02:00
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import org.dom4j.Element;
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import org.dom4j.io.SAXReader;
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2019-12-06 13:38:00 +01:00
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import scala.Tuple2;
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2020-03-20 13:01:56 +01:00
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import java.io.Serializable;
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2020-04-01 18:48:31 +02:00
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import java.io.StringReader;
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import java.util.ArrayList;
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2019-12-06 13:38:00 +01:00
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import java.util.List;
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2020-03-20 13:01:56 +01:00
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public class SparkCreateSimRels implements Serializable {
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2019-12-06 13:38:00 +01:00
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2020-03-20 13:01:56 +01:00
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private static final Log log = LogFactory.getLog(SparkCreateSimRels.class);
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2019-12-06 13:38:00 +01:00
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public static void main(String[] args) throws Exception {
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2020-03-27 10:42:17 +01:00
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(
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SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
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2019-12-06 13:38:00 +01:00
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parser.parseArgument(args);
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2020-03-20 13:01:56 +01:00
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new SparkCreateSimRels().run(parser);
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}
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private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException {
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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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2020-03-20 19:17:24 +01:00
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System.out.println(String.format("graphBasePath: '%s'", graphBasePath));
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System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl));
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System.out.println(String.format("actionSetId: '%s'", actionSetId));
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System.out.println(String.format("workingPath: '%s'", workingPath));
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2020-04-01 18:48:31 +02:00
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List<DedupConfig> configurations = getConfigurations(isLookUpUrl, actionSetId);
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System.out.println("configurations = " + configurations.size());
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// try (SparkSession spark = getSparkSession(parser)) {
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// final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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//
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// //for each dedup configuration
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// for (DedupConfig dedupConf: getConfigurations(isLookUpUrl, 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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//
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// JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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// .mapToPair((PairFunction<String, String, MapDocument>) s -> {
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// MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
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// return new Tuple2<String, MapDocument>(d.getIdentifier(), d);
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// });
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//
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// //create blocks for deduplication
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// JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
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//
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// //create relations by comparing only elements in the same group
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// final JavaPairRDD<String, String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
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//
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// JavaRDD<Relation> relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity));
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//
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// //save the simrel in the workingdir
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// spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class))
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// .write()
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// .mode("overwrite")
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// .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity));
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// }
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// }
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2020-03-20 13:01:56 +01:00
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}
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2020-03-25 14:16:06 +01:00
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/**
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* Utility method used to create an atomic action from a Relation object
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* @param relation input relation
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* @return A tuple2 with [id, json serialization of the atomic action]
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* @throws JsonProcessingException
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*/
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2020-03-20 13:01:56 +01:00
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public Tuple2<Text, Text> createSequenceFileRow(Relation relation) throws JsonProcessingException {
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ObjectMapper mapper = new ObjectMapper();
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String id = relation.getSource() + "@" + relation.getRelClass() + "@" + relation.getTarget();
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AtomicAction<Relation> aa = new AtomicAction<>(Relation.class, relation);
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return new Tuple2<>(
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new Text(id),
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new Text(mapper.writeValueAsString(aa))
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);
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}
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public 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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2019-12-06 13:38:00 +01:00
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2020-03-20 13:01:56 +01:00
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switch(entity){
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case "result":
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r.setRelClass("resultResult_dedupSimilarity_isSimilarTo");
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break;
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case "organization":
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r.setRelClass("organizationOrganization_dedupSimilarity_isSimilarTo");
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break;
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default:
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r.setRelClass("isSimilarTo");
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break;
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}
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return r;
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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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2019-12-06 13:38:00 +01:00
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2020-03-20 13:01:56 +01:00
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return SparkSession
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.builder()
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.appName(SparkCreateSimRels.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.getOrCreate();
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}
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2020-04-01 18:48:31 +02:00
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public List<DedupConfig> getConfigurations(String isLookUpUrl, String orchestrator) throws ISLookUpException, DocumentException {
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final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookUpUrl);
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final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator);
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String orchestratorProfile = isLookUpService.getResourceProfileByQuery(xquery);
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final Document doc = new SAXReader().read(new StringReader(orchestratorProfile));
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final String actionSetId = doc.valueOf("//DEDUPLICATION/ACTION_SET/@id");
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final List<DedupConfig> configurations = new ArrayList<>();
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for (final Object o : doc.selectNodes("//SCAN_SEQUENCE/SCAN")) {
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configurations.add(loadConfig(isLookUpService, actionSetId, o));
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}
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return configurations;
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}
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public DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o)
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throws ISLookUpException {
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final Element s = (Element) o;
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final String configProfileId = s.attributeValue("id");
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final String conf =
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isLookUpService.getResourceProfileByQuery(String.format(
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"for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()",
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configProfileId));
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final DedupConfig dedupConfig = DedupConfig.load(conf);
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dedupConfig.getWf().setConfigurationId(actionSetId);
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return dedupConfig;
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}
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2020-03-20 13:01:56 +01:00
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}
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