forked from antonis.lempesis/dnet-hadoop
implementation of the raw wf for openorgs: still not complete, some functionalities are missing
This commit is contained in:
miconis
parent
112da6d76a
commit
1e1aab83e3
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package eu.dnetlib.dhp.oa.dedup;
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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 org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.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 java.io.IOException;
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import java.util.Optional;
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//copy simrels (verified) from relation to the workdir in order to make them available for the deduplication
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public class SparkCopySimRels extends AbstractSparkAction{
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private static final Logger log = LoggerFactory.getLogger(SparkCopySimRels.class);
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public SparkCopySimRels(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/createSimRels_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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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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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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log.info("numPartitions: '{}'", numPartitions);
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("isLookUpUrl: '{}'", isLookUpUrl);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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// for each dedup configuration
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for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
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final String entity = dedupConf.getWf().getEntityType();
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final String subEntity = dedupConf.getWf().getSubEntityValue();
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log.info("Copying simrels for: '{}'", subEntity);
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final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
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removeOutputDir(spark, outputPath);
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
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JavaRDD<Relation> simRels = spark.read().textFile(relationPath).map(patchRelFn(), Encoders.bean(Relation.class)).toJavaRDD().filter(r -> filterRels(r, entity));
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simRels.saveAsTextFile(outputPath);
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}
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}
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private static MapFunction<String, Relation> patchRelFn() {
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return value -> {
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final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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return rel;
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};
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}
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private boolean filterRels(Relation rel, String entityType) {
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switch(entityType) {
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case "result":
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if (rel.getRelClass().equals("isSimilarTo") && rel.getRelType().equals("resultResult") && rel.getSubRelType().equals("dedup"))
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return true;
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break;
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case "organization":
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if (rel.getRelClass().equals("isSimilarTo") && rel.getRelType().equals("organizationOrganization") && rel.getSubRelType().equals("dedup"))
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return true;
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break;
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default:
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return false;
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}
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return false;
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}
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}
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@ -0,0 +1,233 @@
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package eu.dnetlib.dhp.oa.dedup;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
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import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
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import eu.dnetlib.dhp.oa.dedup.model.Block;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.config.DedupConfig;
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import eu.dnetlib.pace.model.MapDocument;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import 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.MapFunction;
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import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.graphx.Edge;
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import org.apache.spark.rdd.RDD;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.DocumentException;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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import java.io.IOException;
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import java.util.*;
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import java.util.stream.Collectors;
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import java.util.stream.StreamSupport;
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import static eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels.DNET_PROVENANCE_ACTIONS;
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import static eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels.PROVENANCE_ACTION_CLASS;
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import static eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels.hash;
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public class SparkRemoveDiffRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkRemoveDiffRels.class);
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public SparkRemoveDiffRels(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/createSimRels_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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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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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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log.info("numPartitions: '{}'", numPartitions);
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("isLookUpUrl: '{}'", isLookUpUrl);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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// for each dedup configuration
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for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
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final String entity = dedupConf.getWf().getEntityType();
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final String subEntity = dedupConf.getWf().getSubEntityValue();
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log.info("Removing diffrels for: '{}'", subEntity);
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final String mergeRelsPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity);
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
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final int maxIterations = dedupConf.getWf().getMaxIterations();
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log.info("Max iterations {}", maxIterations);
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JavaRDD<Relation> mergeRelsRDD = spark
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.read()
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.load(mergeRelsPath)
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.as(Encoders.bean(Relation.class))
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.where("relClass == 'merges'")
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.toJavaRDD();
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JavaRDD<Tuple2<Tuple2<String, String>, String>> diffRelsRDD = spark
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.read()
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.textFile(relationPath)
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.map(patchRelFn(), Encoders.bean(Relation.class))
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.toJavaRDD().filter(r -> filterRels(r, entity))
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.map(rel -> {
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if (rel.getSource().compareTo(rel.getTarget()) < 0)
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return new Tuple2<>(new Tuple2<>(rel.getSource(), rel.getTarget()), "diffRel");
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else
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return new Tuple2<>(new Tuple2<>(rel.getTarget(), rel.getSource()), "diffRel");
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});
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JavaRDD<Tuple2<Tuple2<String, String>, String>> flatMergeRels = mergeRelsRDD
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.mapToPair(rel -> new Tuple2<>(rel.getSource(), rel.getTarget()))
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.groupByKey()
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.flatMap(g -> {
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List<Tuple2<Tuple2<String,String>, String>> rels = new ArrayList<>();
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List<String> ids = StreamSupport
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.stream(g._2().spliterator(), false)
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.collect(Collectors.toList());
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for (int i = 0; i < ids.size(); i++){
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for (int j = i+1; j < ids.size(); j++){
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if (ids.get(i).compareTo(ids.get(j)) < 0)
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rels.add(new Tuple2<>(new Tuple2<>(ids.get(i), ids.get(j)), g._1()));
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else
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rels.add(new Tuple2<>(new Tuple2<>(ids.get(j), ids.get(i)), g._1()));
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}
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}
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return rels.iterator();
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});
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JavaRDD<Relation> purgedMergeRels = flatMergeRels.union(diffRelsRDD)
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.mapToPair(rel -> new Tuple2<>(rel._1(), Arrays.asList(rel._2())))
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.reduceByKey((a, b) -> {
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List<String> list = new ArrayList<String>();
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list.addAll(a);
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list.addAll(b);
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return list;
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})
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.filter(rel -> rel._2().size() == 1)
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.mapToPair(rel -> new Tuple2<>(rel._2().get(0), rel._1()))
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.flatMap(rel -> {
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List<Tuple2<String, String>> rels = new ArrayList<>();
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String source = rel._1();
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rels.add(new Tuple2<>(source, rel._2()._1()));
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rels.add(new Tuple2<>(source, rel._2()._2()));
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return rels.iterator();
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})
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.distinct()
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.flatMap(rel -> tupleToMergeRel(rel, dedupConf));
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spark
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.createDataset(purgedMergeRels.rdd(), Encoders.bean(Relation.class))
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.write()
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.mode(SaveMode.Overwrite).parquet(mergeRelsPath);
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}
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}
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private static MapFunction<String, Relation> patchRelFn() {
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return value -> {
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final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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return rel;
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};
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}
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private boolean filterRels(Relation rel, String entityType) {
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switch(entityType) {
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case "result":
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if (rel.getRelClass().equals("isDifferentFrom") && rel.getRelType().equals("resultResult") && rel.getSubRelType().equals("dedup"))
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return true;
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break;
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case "organization":
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if (rel.getRelClass().equals("isDifferentFrom") && rel.getRelType().equals("organizationOrganization") && rel.getSubRelType().equals("dedup"))
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return true;
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break;
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default:
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return false;
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}
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return false;
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}
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public Iterator<Relation> tupleToMergeRel(Tuple2<String, String> rel, DedupConfig dedupConf) {
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List<Relation> rels = new ArrayList<>();
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rels.add(rel(rel._1(), rel._2(), "merges", dedupConf));
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rels.add(rel(rel._2(), rel._1(), "isMergedIn", dedupConf));
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return rels.iterator();
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}
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private Relation rel(String source, String target, String relClass, DedupConfig dedupConf) {
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String entityType = dedupConf.getWf().getEntityType();
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Relation r = new Relation();
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r.setSource(source);
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r.setTarget(target);
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r.setRelClass(relClass);
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r.setRelType(entityType + entityType.substring(0, 1).toUpperCase() + entityType.substring(1));
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r.setSubRelType("dedup");
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DataInfo info = new DataInfo();
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info.setDeletedbyinference(false);
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info.setInferred(true);
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info.setInvisible(false);
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info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
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Qualifier provenanceAction = new Qualifier();
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provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
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provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
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provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
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provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
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info.setProvenanceaction(provenanceAction);
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// TODO calculate the trust value based on the similarity score of the elements in the CC
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// info.setTrust();
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r.setDataInfo(info);
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return r;
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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>
|
||||||
|
</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>
|
||||||
|
|
@ -0,0 +1,324 @@
|
||||||
|
<workflow-app name="Openorgs 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>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="resetOrgSimRels">
|
||||||
|
<fs>
|
||||||
|
<delete path="${workingPath}/${actionSetId}/organization_simrel"/>
|
||||||
|
</fs>
|
||||||
|
<ok to="copySimRels"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<!--extract simrels from relations and copy into the organization_simrel-->
|
||||||
|
<action name="copySimRels">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Copy Similarity Relations</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.dedup.SparkCopySimRels</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>${actionSetId}</arg>
|
||||||
|
<arg>--numPartitions</arg><arg>8000</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="CreateDedupRecord"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<!-- il root record è openorgs, le simrel fra le openorgs e gli altri record restano -->
|
||||||
|
<!-- per le organizzazioni: openorgs SOLO QUELLE VALIDATE, altre TUTTE -->
|
||||||
|
<!--create the deduprecords using relations taken from openorgs: CHECK IF IT WORKS -->
|
||||||
|
<action name="CreateDedupRecord">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Create Dedup Record</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.dedup.SparkCreateDedupRecord</class>
|
||||||
|
<jar>dhp-dedup-openaire-${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>
|
||||||
|
</spark>
|
||||||
|
<ok to="UpdateEntity"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="UpdateEntity">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Update Entity</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.dedup.SparkUpdateEntity</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>${workingPath}</arg>
|
||||||
|
<arg>--dedupGraphPath</arg><arg>${dedupGraphPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="CreateSimRels"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="CreateSimRels">
|
||||||
|
<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>${workingPath}</arg>
|
||||||
|
<arg>--numPartitions</arg><arg>8000</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="CreateMergeRels"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="CreateMergeRels">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Create Merge Relations</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels</class>
|
||||||
|
<jar>dhp-dedup-openaire-${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>${cutConnectedComponent}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="RemoveDifferences"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="RemoveDifferences">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Create Merge Relations</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.dedup.SparkRemoveDiffRels</class>
|
||||||
|
<jar>dhp-dedup-openaire-${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="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>
|
||||||
Loading…
Reference in New Issue