forked from D-Net/dnet-hadoop
implementation of a new workflow to compute statistics on the blocks
This commit is contained in:
miconis
parent
2c4ed9a043
commit
9258e4f095
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@ -100,6 +100,11 @@ public class DedupUtility {
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return String.format("%s/%s/%s_mergerel", basePath, actionSetId, entityType);
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return String.format("%s/%s/%s_mergerel", basePath, actionSetId, entityType);
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}
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}
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public static String createBlockStatsPath(
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final String basePath, final String actionSetId, final String entityType) {
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return String.format("%s/%s/%s_blockstats", basePath, actionSetId, entityType);
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}
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public static List<DedupConfig> getConfigurations(String isLookUpUrl, String orchestrator)
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public static List<DedupConfig> getConfigurations(String isLookUpUrl, String orchestrator)
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throws ISLookUpException, DocumentException {
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throws ISLookUpException, DocumentException {
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final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookUpUrl);
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final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookUpUrl);
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@ -0,0 +1,121 @@
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package eu.dnetlib.dhp.oa.dedup;
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import java.io.IOException;
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import eu.dnetlib.dhp.oa.dedup.model.BlockStats;
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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.PairFunction;
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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 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.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.FieldListImpl;
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import eu.dnetlib.pace.model.FieldValueImpl;
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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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public class SparkBlockStats extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
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public SparkBlockStats(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/createBlockStats_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf
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.registerKryoClasses(
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new Class[] {
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MapDocument.class, FieldListImpl.class, FieldValueImpl.class, Block.class
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});
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new SparkCreateSimRels(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@Override
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public void run(ISLookUpService isLookUpService)
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throws DocumentException, IOException, ISLookUpException {
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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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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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// for each dedup configuration
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for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
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final String subEntity = dedupConf.getWf().getSubEntityValue();
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log.info("Creating blockstats for: '{}'", subEntity);
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final String outputPath = DedupUtility.createBlockStatsPath(workingPath, actionSetId, subEntity);
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removeOutputDir(spark, outputPath);
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaPairRDD<String, MapDocument> mapDocuments = sc
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.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.mapToPair(
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(PairFunction<String, String, MapDocument>) s -> {
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MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
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return new Tuple2<>(d.getIdentifier(), d);
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});
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// create blocks for deduplication
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JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf);
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JavaRDD<BlockStats> blockStats = blocks.map(b ->
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new BlockStats(
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b._1(),
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(long) b._2().getDocuments().size(),
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computeComparisons(
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(long) b._2().getDocuments().size(), (long) dedupConf.getWf().getSlidingWindowSize()))
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);
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// save the blockstats in the workingdir
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spark
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.createDataset(blockStats.rdd(), Encoders.bean(BlockStats.class))
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.write()
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.mode(SaveMode.Overwrite)
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.save(outputPath);
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}
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}
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public Long computeComparisons(Long blockSize, Long slidingWindowSize){
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if (slidingWindowSize >= blockSize)
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return (slidingWindowSize * (slidingWindowSize - 1)) / 2;
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else {
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return (blockSize - slidingWindowSize + 1) * (slidingWindowSize * (slidingWindowSize - 1)) / 2;
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}
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}
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}
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@ -0,0 +1,42 @@
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package eu.dnetlib.dhp.oa.dedup.model;
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public class BlockStats {
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private String key; //key of the block
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private Long size; //number of elements in the block
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private Long comparisons; //number of comparisons in the block
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public BlockStats() {
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}
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public BlockStats(String key, Long size, Long comparisons) {
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this.key = key;
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this.size = size;
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this.comparisons = comparisons;
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}
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public String getKey() {
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return key;
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}
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public void setKey(String key) {
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this.key = key;
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}
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public Long getSize() {
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return size;
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}
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public void setSize(Long size) {
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this.size = size;
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}
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public Long getComparisons() {
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return comparisons;
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}
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public void setComparisons(Long comparisons) {
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this.comparisons = comparisons;
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}
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}
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@ -0,0 +1,26 @@
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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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@ -0,0 +1,18 @@
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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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@ -0,0 +1,111 @@
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<workflow-app name="Duplicate Scan" 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>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>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="CreateBlockStats"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="CreateBlockStats">
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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.SparkBlockStats</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}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=3840
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</spark-opts>
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<arg>--i</arg><arg>${graphBasePath}</arg>
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<arg>--la</arg><arg>${isLookUpUrl}</arg>
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<arg>--asi</arg><arg>${actionSetId}</arg>
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<arg>--w</arg><arg>${workingPath}</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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