code refactoring (useless classes and wf removed), implementation of the test for the openorgs dedup
miconis
3 years ago
parent
2355cc4e9b
commit
f446580e9f
@ -1,184 +0,0 @@
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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.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import java.util.stream.StreamSupport;
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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.sql.*;
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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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.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 scala.Tuple2;
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public class SparkCollectSimRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCollectSimRels.class);
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Dataset<Row> simGroupsDS;
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Dataset<Row> groupsDS;
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public SparkCollectSimRels(ArgumentApplicationParser parser, SparkSession spark, Dataset<Row> simGroupsDS,
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Dataset<Row> groupsDS) {
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super(parser, spark);
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this.simGroupsDS = simGroupsDS;
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this.groupsDS = groupsDS;
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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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SparkBlockStats.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/collectSimRels_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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final String dbUrl = parser.get("postgresUrl");
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final String dbUser = parser.get("postgresUser");
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final String dbPassword = parser.get("postgresPassword");
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SparkSession spark = getSparkSession(conf);
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DataFrameReader readOptions = spark
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.read()
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.format("jdbc")
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.option("url", dbUrl)
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.option("user", dbUser)
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.option("password", dbPassword);
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new SparkCollectSimRels(
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parser,
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spark,
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readOptions.option("dbtable", "similarity_groups").load(),
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readOptions.option("dbtable", "groups").load())
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@Override
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void run(ISLookUpService isLookUpService) throws DocumentException, ISLookUpException, IOException {
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// read oozie parameters
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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 dbUrl = parser.get("postgresUrl");
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final String dbUser = parser.get("postgresUser");
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log.info("numPartitions: '{}'", numPartitions);
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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("postgresUser: {}", dbUser);
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log.info("postgresUrl: {}", dbUrl);
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log.info("postgresPassword: xxx");
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JavaPairRDD<String, List<String>> similarityGroup = simGroupsDS
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.toJavaRDD()
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.mapToPair(r -> new Tuple2<>(r.getString(0), r.getString(1)))
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.groupByKey()
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.mapToPair(
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i -> new Tuple2<>(i._1(), StreamSupport
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.stream(i._2().spliterator(), false)
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.collect(Collectors.toList())));
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JavaPairRDD<String, String> groupIds = groupsDS
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.toJavaRDD()
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.mapToPair(r -> new Tuple2<>(r.getString(0), r.getString(1)));
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JavaRDD<Tuple2<Tuple2<String, String>, List<String>>> groups = similarityGroup
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.leftOuterJoin(groupIds)
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.filter(g -> g._2()._2().isPresent())
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.map(g -> new Tuple2<>(new Tuple2<>(g._1(), g._2()._2().get()), g._2()._1()));
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JavaRDD<Relation> relations = groups.flatMap(g -> {
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String firstId = g._2().get(0);
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List<Relation> rels = new ArrayList<>();
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for (String id : g._2()) {
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if (!firstId.equals(id))
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rels.add(createSimRel(firstId, id, g._1()._2()));
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}
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return rels.iterator();
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});
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Dataset<Relation> resultRelations = spark
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.createDataset(
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relations.filter(r -> r.getRelType().equals("resultResult")).rdd(),
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Encoders.bean(Relation.class))
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.repartition(numPartitions);
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Dataset<Relation> organizationRelations = spark
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.createDataset(
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relations.filter(r -> r.getRelType().equals("organizationOrganization")).rdd(),
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Encoders.bean(Relation.class))
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.repartition(numPartitions);
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for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
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switch (dedupConf.getWf().getSubEntityValue()) {
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case "organization":
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savePostgresRelation(organizationRelations, workingPath, actionSetId, "organization");
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break;
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default:
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savePostgresRelation(
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resultRelations, workingPath, actionSetId, dedupConf.getWf().getSubEntityValue());
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break;
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}
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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.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.setSource("50|" + source);
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r.setTarget("50|" + target);
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r.setRelType("resultResult");
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break;
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case "organization":
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r.setSource("20|" + source);
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r.setTarget("20|" + target);
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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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private void savePostgresRelation(Dataset<Relation> newRelations, String workingPath, String actionSetId,
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String entityType) {
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newRelations
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.write()
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.mode(SaveMode.Append)
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.parquet(DedupUtility.createSimRelPath(workingPath, actionSetId, entityType));
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}
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}
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@ -1,44 +0,0 @@
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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": "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": "purl",
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"paramLongName": "postgresUrl",
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"paramDescription": "the url of the postgres server",
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"paramRequired": true
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},
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{
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"paramName": "pusr",
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"paramLongName": "postgresUser",
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"paramDescription": "the owner of the postgres database",
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"paramRequired": true
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},
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{
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"paramName": "ppwd",
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"paramLongName": "postgresPassword",
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"paramDescription": "the password for the postgres user",
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"paramRequired": true
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}
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]
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@ -1,18 +0,0 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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</configuration>
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@ -1,208 +0,0 @@
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<workflow-app name="Organization Dedup" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>graphBasePath</name>
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<description>the raw graph base path</description>
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</property>
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<property>
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<name>isLookUpUrl</name>
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<description>the address of the lookUp service</description>
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</property>
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<property>
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<name>actionSetId</name>
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<description>id of the actionSet</description>
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</property>
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<property>
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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>dedupGraphPath</name>
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<description>path for the output graph</description>
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</property>
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<property>
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<name>cutConnectedComponent</name>
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<description>max number of elements in a connected component</description>
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</property>
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<property>
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<name>dbUrl</name>
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<description>the url of the database</description>
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</property>
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<property>
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<name>dbUser</name>
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<description>the user of the database</description>
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</property>
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<property>
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<name>dbTable</name>
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<description>the name of the table in the database</description>
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</property>
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<property>
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<name>dbPwd</name>
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<description>the passowrd of the user of the database</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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<description>spark 2.* extra listeners classname</description>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</description>
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="resetWorkingPath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="resetWorkingPath">
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<fs>
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<delete path="${workingPath}"/>
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</fs>
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<ok to="copyRelations"/>
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<error to="Kill"/>
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</action>
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<action name="copyRelations">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<arg>-pb</arg>
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<arg>${graphBasePath}/relation</arg>
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<arg>${workingPath}/${actionSetId}/organization_simrel</arg>
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</distcp>
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<ok to="CreateSimRel"/>
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<error to="Kill"/>
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</action>
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<action name="CreateSimRel">
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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>Create Similarity Relations</name>
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<class>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</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>${workingPath}</arg>
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<arg>--numPartitions</arg><arg>8000</arg>
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</spark>
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<ok to="CreateMergeRel"/>
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<error to="Kill"/>
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</action>
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<action name="CreateMergeRel">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Create Merge Relations</name>
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<class>eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels</class>
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<jar>dhp-dedup-openaire-${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>${graphBasePath}</arg>
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<arg>--workingPath</arg><arg>${workingPath}</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>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
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</spark>
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<ok to="PrepareNewOrgs"/>
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<error to="Kill"/>
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</action>
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<action name="PrepareNewOrgs">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Prepare New Organizations</name>
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<class>eu.dnetlib.dhp.oa.dedup.SparkPrepareNewOrgs</class>
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<jar>dhp-dedup-openaire-${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>${graphBasePath}</arg>
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<arg>--workingPath</arg><arg>${workingPath}</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>--dbUrl</arg><arg>${dbUrl}</arg>
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<arg>--dbTable</arg><arg>${dbTable}</arg>
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<arg>--dbUser</arg><arg>${dbUser}</arg>
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<arg>--dbPwd</arg><arg>${dbPwd}</arg>
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<arg>--numConnections</arg><arg>20</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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@ -1,18 +0,0 @@
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<configuration>
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<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
</configuration>
|
||||
@ -1,240 +0,0 @@
|
||||
<workflow-app name="Organization Dedup" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>graphBasePath</name>
|
||||
<description>the raw graph base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>isLookUpUrl</name>
|
||||
<description>the address of the lookUp service</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>actionSetId</name>
|
||||
<description>id of the actionSet</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>path for the working directory</description>
|
||||
</property>
|
||||
<property>
|
||||
<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>dbUrl</name>
|
||||
<description>the url of the database</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>dbUser</name>
|
||||
<description>the user of the database</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>dbTable</name>
|
||||
<description>the name of the table in the database</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>dbPwd</name>
|
||||
<description>the passowrd of the user of the database</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozieActionShareLibForSpark2</name>
|
||||
<description>oozie action sharelib for spark 2.*</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||
<description>spark 2.* extra listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||
<description>spark 2.* sql query execution listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<description>spark 2.* yarn history server address</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<description>spark 2.* event log dir location</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>mapreduce.job.queuename</name>
|
||||
<value>${queueName}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapred.job.queue.name</name>
|
||||
<value>${oozieLauncherQueueName}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="resetWorkingPath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="resetWorkingPath">
|
||||
<fs>
|
||||
<delete path="${workingPath}"/>
|
||||
</fs>
|
||||
<ok to="copyRelations"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copyRelations">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>-pb</arg>
|
||||
<arg>/tmp/graph_openorgs_and_corda/relation</arg>
|
||||
<arg>${workingPath}/${actionSetId}/organization_simrel</arg>
|
||||
</distcp>
|
||||
<ok to="CreateSimRel"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="CreateSimRel">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Create Similarity Relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<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"/>
|
||||
</action>
|
||||
|
||||
<action name="CreateMergeRel">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Create Merge Relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphBasePath</arg><arg>${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="PrepareOrgRels"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="PrepareOrgRels">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Prepare Organization Relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.SparkPrepareOrgRels</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--dbUrl</arg><arg>${dbUrl}</arg>
|
||||
<arg>--dbTable</arg><arg>${dbTable}</arg>
|
||||
<arg>--dbUser</arg><arg>${dbUser}</arg>
|
||||
<arg>--dbPwd</arg><arg>${dbPwd}</arg>
|
||||
<arg>--numConnections</arg><arg>20</arg>
|
||||
</spark>
|
||||
<ok to="PrepareNewOrgs"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="PrepareNewOrgs">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Prepare New Organizations</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.SparkPrepareNewOrgs</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<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>--apiUrl</arg><arg>${apiUrl}</arg>
|
||||
<arg>--dbUrl</arg><arg>${dbUrl}</arg>
|
||||
<arg>--dbTable</arg><arg>${dbTable}</arg>
|
||||
<arg>--dbUser</arg><arg>${dbUser}</arg>
|
||||
<arg>--dbPwd</arg><arg>${dbPwd}</arg>
|
||||
<arg>--numConnections</arg><arg>20</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
@ -0,0 +1,408 @@
|
||||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
|
||||
import static org.apache.spark.sql.functions.count;
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Paths;
|
||||
import java.sql.Connection;
|
||||
import java.sql.DriverManager;
|
||||
import java.sql.ResultSet;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
import java.util.Properties;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
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.ForeachFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.PairFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.apache.spark.util.CollectionsUtils;
|
||||
import org.junit.jupiter.api.*;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.junit.platform.commons.util.StringUtils;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.Mockito;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafMapperUtils;
|
||||
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import scala.Tuple2;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
public class SparkOpenorgsDedupTest implements Serializable {
|
||||
|
||||
private static String dbUrl = "jdbc:h2:mem:openorgs_test;DB_CLOSE_DELAY=-1;DATABASE_TO_UPPER=false";
|
||||
private static String dbUser = "sa";
|
||||
private static String dbTable = "tmp_dedup_events";
|
||||
private static String dbPwd = "";
|
||||
|
||||
@Mock(serializable = true)
|
||||
ISLookUpService isLookUpService;
|
||||
|
||||
protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
private static SparkSession spark;
|
||||
private static JavaSparkContext jsc;
|
||||
|
||||
private static String testGraphBasePath;
|
||||
private static String testOutputBasePath;
|
||||
private static String testDedupGraphBasePath;
|
||||
private static final String testActionSetId = "test-orchestrator-openorgs";
|
||||
|
||||
@BeforeAll
|
||||
public static void cleanUp() throws IOException, URISyntaxException {
|
||||
|
||||
testGraphBasePath = Paths
|
||||
.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/openorgs_dedup").toURI())
|
||||
.toFile()
|
||||
.getAbsolutePath();
|
||||
testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
|
||||
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(conf)
|
||||
.getOrCreate();
|
||||
|
||||
jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
}
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() throws IOException, ISLookUpException {
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_openorgs.xml")));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(1)
|
||||
public void createSimRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
|
||||
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-la", "lookupurl",
|
||||
"-w", testOutputBasePath,
|
||||
"-np", "50"
|
||||
});
|
||||
|
||||
new SparkCreateSimRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_simrel = spark
|
||||
.read()
|
||||
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
|
||||
.count();
|
||||
|
||||
assertEquals(288, orgs_simrel);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(2)
|
||||
public void copyOpenorgsSimRels() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCopyOpenorgsSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-w", testOutputBasePath,
|
||||
"-la", "lookupurl",
|
||||
"-np", "50"
|
||||
});
|
||||
|
||||
new SparkCopyOpenorgsSimRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_simrel = spark
|
||||
.read()
|
||||
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
|
||||
.count();
|
||||
|
||||
assertEquals(324, orgs_simrel);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(3)
|
||||
public void createMergeRelsTest() 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
|
||||
});
|
||||
|
||||
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_mergerel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
||||
.count();
|
||||
assertEquals(132, orgs_mergerel);
|
||||
|
||||
// verify that a DiffRel is in the mergerels (to be sure that the job supposed to remove them has something to
|
||||
// do)
|
||||
List<String> diffRels = jsc
|
||||
.textFile(DedupUtility.createEntityPath(testGraphBasePath, "relation"))
|
||||
.map(s -> OBJECT_MAPPER.readValue(s, Relation.class))
|
||||
.filter(r -> r.getRelClass().equals("isDifferentFrom"))
|
||||
.map(r -> r.getTarget())
|
||||
.collect();
|
||||
assertEquals(18, diffRels.size());
|
||||
|
||||
List<String> mergeRels = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.map(r -> r.getTarget())
|
||||
.collect();
|
||||
assertFalse(Collections.disjoint(mergeRels, diffRels));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(4)
|
||||
public void prepareOrgRelsTest() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/prepareOrgRels_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i",
|
||||
testGraphBasePath,
|
||||
"-asi",
|
||||
testActionSetId,
|
||||
"-la",
|
||||
"lookupurl",
|
||||
"-w",
|
||||
testOutputBasePath,
|
||||
"-du",
|
||||
dbUrl,
|
||||
"-dusr",
|
||||
dbUser,
|
||||
"-t",
|
||||
dbTable,
|
||||
"-dpwd",
|
||||
dbPwd
|
||||
});
|
||||
|
||||
new SparkPrepareOrgRels(parser, spark).run(isLookUpService);
|
||||
|
||||
final Properties connectionProperties = new Properties();
|
||||
connectionProperties.put("user", dbUser);
|
||||
connectionProperties.put("password", dbPwd);
|
||||
|
||||
Connection connection = DriverManager.getConnection(dbUrl, connectionProperties);
|
||||
|
||||
ResultSet resultSet = connection
|
||||
.prepareStatement("SELECT COUNT(*) as total_rels FROM " + dbTable)
|
||||
.executeQuery();
|
||||
if (resultSet.next()) {
|
||||
int total_rels = resultSet.getInt("total_rels");
|
||||
assertEquals(32, total_rels);
|
||||
} else
|
||||
fail("No result in the sql DB");
|
||||
resultSet.close();
|
||||
|
||||
// verify the number of organizations with duplicates
|
||||
ResultSet resultSet2 = connection
|
||||
.prepareStatement("SELECT COUNT(DISTINCT(local_id)) as total_orgs FROM " + dbTable)
|
||||
.executeQuery();
|
||||
if (resultSet2.next()) {
|
||||
int total_orgs = resultSet2.getInt("total_orgs");
|
||||
assertEquals(6, total_orgs);
|
||||
} else
|
||||
fail("No result in the sql DB");
|
||||
resultSet2.close();
|
||||
|
||||
// verify that no DiffRel is in the DB
|
||||
List<String> diffRels = jsc
|
||||
.textFile(DedupUtility.createEntityPath(testGraphBasePath, "relation"))
|
||||
.map(s -> OBJECT_MAPPER.readValue(s, Relation.class))
|
||||
.filter(r -> r.getRelClass().equals("isDifferentFrom"))
|
||||
.map(r -> r.getSource() + "@@@" + r.getTarget())
|
||||
.collect();
|
||||
|
||||
List<String> dbRels = new ArrayList<>();
|
||||
ResultSet resultSet3 = connection
|
||||
.prepareStatement("SELECT local_id, oa_original_id FROM " + dbTable)
|
||||
.executeQuery();
|
||||
while (resultSet3.next()) {
|
||||
String source = OafMapperUtils.createOpenaireId("organization", resultSet3.getString("local_id"), true);
|
||||
String target = OafMapperUtils
|
||||
.createOpenaireId("organization", resultSet3.getString("oa_original_id"), true);
|
||||
dbRels.add(source + "@@@" + target);
|
||||
}
|
||||
resultSet3.close();
|
||||
assertTrue(Collections.disjoint(dbRels, diffRels));
|
||||
|
||||
connection.close();
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(5)
|
||||
public void prepareNewOrgsTest() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/prepareNewOrgs_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i",
|
||||
testGraphBasePath,
|
||||
"-asi",
|
||||
testActionSetId,
|
||||
"-la",
|
||||
"lookupurl",
|
||||
"-w",
|
||||
testOutputBasePath,
|
||||
"-du",
|
||||
dbUrl,
|
||||
"-dusr",
|
||||
dbUser,
|
||||
"-t",
|
||||
dbTable,
|
||||
"-dpwd",
|
||||
dbPwd
|
||||
});
|
||||
|
||||
new SparkPrepareNewOrgs(parser, spark).run(isLookUpService);
|
||||
|
||||
final Properties connectionProperties = new Properties();
|
||||
connectionProperties.put("user", dbUser);
|
||||
connectionProperties.put("password", dbPwd);
|
||||
|
||||
long orgs_in_diffrel = jsc
|
||||
.textFile(DedupUtility.createEntityPath(testGraphBasePath, "relation"))
|
||||
.map(s -> OBJECT_MAPPER.readValue(s, Relation.class))
|
||||
.filter(r -> r.getRelClass().equals("isDifferentFrom"))
|
||||
.map(r -> r.getTarget())
|
||||
.distinct()
|
||||
.count();
|
||||
|
||||
Connection connection = DriverManager.getConnection(dbUrl, connectionProperties);
|
||||
|
||||
jsc
|
||||
.textFile(DedupUtility.createEntityPath(testGraphBasePath, "relation"))
|
||||
.map(s -> OBJECT_MAPPER.readValue(s, Relation.class))
|
||||
.filter(r -> r.getRelClass().equals("isDifferentFrom"))
|
||||
.map(r -> r.getTarget())
|
||||
.distinct()
|
||||
.foreach(s -> System.out.println("difforgs = " + s));
|
||||
ResultSet resultSet0 = connection
|
||||
.prepareStatement("SELECT oa_original_id FROM " + dbTable + " WHERE local_id = ''")
|
||||
.executeQuery();
|
||||
while (resultSet0.next())
|
||||
System.out
|
||||
.println(
|
||||
"dborgs = " + OafMapperUtils.createOpenaireId(20, resultSet0.getString("oa_original_id"), true));
|
||||
resultSet0.close();
|
||||
|
||||
ResultSet resultSet = connection
|
||||
.prepareStatement("SELECT COUNT(*) as total_new_orgs FROM " + dbTable + " WHERE local_id = ''")
|
||||
.executeQuery();
|
||||
if (resultSet.next()) {
|
||||
int total_new_orgs = resultSet.getInt("total_new_orgs");
|
||||
assertEquals(orgs_in_diffrel + 1, total_new_orgs);
|
||||
} else
|
||||
fail("No result in the sql DB");
|
||||
resultSet.close();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void finalCleanUp() throws IOException {
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
}
|
||||
|
||||
}
|
||||
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Loading…
Reference in New Issue