forked from D-Net/dnet-hadoop
relation consistency workflow separated from dedup scan and creation of CCs
This commit is contained in:
parent
c92bfeeaee
commit
038ac7afd7
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@ -22,6 +22,21 @@ public class HdfsSupport {
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private HdfsSupport() {
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}
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/**
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* Checks a path (file or dir) exists on HDFS.
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*
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* @param path Path to be checked
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* @param configuration Configuration of hadoop env
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*/
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public static boolean exists(String path, Configuration configuration) {
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logger.info("Removing path: {}", path);
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return rethrowAsRuntimeException(() -> {
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Path f = new Path(path);
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FileSystem fileSystem = FileSystem.get(configuration);
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return fileSystem.exists(f);
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});
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}
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/**
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* Removes a path (file or dir) from HDFS.
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*
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@ -99,6 +99,8 @@ public class PartitionActionSetsByPayloadTypeJob {
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List<String> inputActionSetPaths,
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String outputPath) {
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inputActionSetPaths
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.stream()
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.filter(path -> HdfsSupport.exists(path, spark.sparkContext().hadoopConfiguration()))
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.forEach(inputActionSetPath -> {
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Dataset<Row> actionDS = readActionSetFromPath(spark, inputActionSetPath);
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saveActions(actionDS, outputPath);
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@ -1,7 +1,9 @@
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package eu.dnetlib.dhp.oa.dedup;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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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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@ -21,6 +23,9 @@ import java.util.List;
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abstract class AbstractSparkAction implements Serializable {
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protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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public ArgumentApplicationParser parser; //parameters for the spark action
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public SparkSession spark; //the spark session
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@ -108,4 +113,8 @@ abstract class AbstractSparkAction implements Serializable {
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.config(conf)
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.getOrCreate();
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}
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protected static void removeOutputDir(SparkSession spark, String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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}
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@ -1,6 +1,5 @@
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package eu.dnetlib.dhp.oa.dedup;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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@ -42,26 +41,27 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
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final String actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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System.out.println(String.format("graphBasePath: '%s'", graphBasePath));
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System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl));
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System.out.println(String.format("actionSetId: '%s'", actionSetId));
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System.out.println(String.format("workingPath: '%s'", workingPath));
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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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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) {
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String subEntity = dedupConf.getWf().getSubEntityValue();
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System.out.println(String.format("Creating deduprecords for: '%s'", subEntity));
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log.info("Creating deduprecords for: '{}'", subEntity);
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final String outputPath = DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity);
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removeOutputDir(spark, outputPath);
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final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity);
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final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
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final OafEntityType entityType = OafEntityType.valueOf(subEntity);
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final JavaRDD<OafEntity> dedupRecord =
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DedupRecordFactory.createDedupRecord(sc, spark, mergeRelPath, entityPath, entityType, dedupConf);
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dedupRecord.map(r -> {
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ObjectMapper mapper = new ObjectMapper();
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return mapper.writeValueAsString(r);
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}).saveAsTextFile(DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity));
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dedupRecord.map(r -> OBJECT_MAPPER.writeValueAsString(r)).saveAsTextFile(outputPath);
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}
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}
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@ -4,6 +4,8 @@ import com.google.common.hash.Hashing;
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import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
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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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@ -19,6 +21,7 @@ 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 scala.Tuple2;
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@ -32,7 +35,9 @@ import java.util.List;
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public class SparkCreateMergeRels extends AbstractSparkAction {
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public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
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private static final Logger log = LoggerFactory.getLogger(SparkCreateMergeRels.class);
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public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
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public SparkCreateMergeRels(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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@ -44,7 +49,10 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
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SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
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parser.parseArgument(args);
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new SparkCreateMergeRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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final String isLookUpUrl = parser.get("isLookUpUrl");
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log.info("isLookupUrl {}", isLookUpUrl);
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new SparkCreateMergeRels(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(isLookUpUrl));
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}
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@Override
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@ -55,55 +63,91 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
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final String isLookUpUrl = parser.get("isLookUpUrl");
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final String actionSetId = parser.get("actionSetId");
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System.out.println(String.format("graphBasePath: '%s'", graphBasePath));
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System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl));
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System.out.println(String.format("actionSetId: '%s'", actionSetId));
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System.out.println(String.format("workingPath: '%s'", workingPath));
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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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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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for (DedupConfig dedupConf: getConfigurations(isLookUpService, actionSetId)) {
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final String subEntity = dedupConf.getWf().getSubEntityValue();
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System.out.println(String.format("Creating mergerels for: '%s'", subEntity));
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log.info("Creating mergerels for: '{}'", subEntity);
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final int maxIterations = dedupConf.getWf().getMaxIterations();
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log.info("Max iterations {}", maxIterations);
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final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity);
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final JavaPairRDD<Object, String> vertexes = sc.textFile(graphBasePath + "/" + subEntity)
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.map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s))
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.mapToPair((PairFunction<String, Object, String>)
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s -> new Tuple2<Object, String>(getHashcode(s), s)
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);
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s -> new Tuple2<>(getHashcode(s), s));
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final Dataset<Relation> similarityRelations = spark.read().load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class));
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final RDD<Edge<String>> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd();
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final JavaRDD<ConnectedComponent> cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD();
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final Dataset<Relation> mergeRelation = spark.createDataset(cc.filter(k -> k.getDocIds().size() > 1)
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.flatMap(this::ccToMergeRel).rdd(), Encoders.bean(Relation.class));
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final Dataset<Relation> similarityRelations = spark
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.read()
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.load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity))
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.as(Encoders.bean(Relation.class));
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mergeRelation
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.write().mode("overwrite")
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.save(DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity));
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final RDD<Edge<String>> edgeRdd = similarityRelations
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.javaRDD()
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.map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass()))
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.rdd();
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final RDD<Relation> connectedComponents = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, maxIterations)
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.toJavaRDD()
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.filter(k -> k.getDocIds().size() > 1)
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.flatMap(cc -> ccToMergeRel(cc, dedupConf))
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.rdd();
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spark
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.createDataset(connectedComponents, Encoders.bean(Relation.class))
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.write()
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.mode(SaveMode.Append)
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.save(mergeRelPath);
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}
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}
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public Iterator<Relation> ccToMergeRel(ConnectedComponent cc){
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public Iterator<Relation> ccToMergeRel(ConnectedComponent cc, DedupConfig dedupConf){
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return cc.getDocIds()
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.stream()
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.flatMap(id -> {
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List<Relation> tmp = new ArrayList<>();
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Relation r = new Relation();
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r.setSource(cc.getCcId());
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r.setTarget(id);
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r.setRelClass("merges");
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tmp.add(r);
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r = new Relation();
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r.setTarget(cc.getCcId());
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r.setSource(id);
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r.setRelClass("isMergedIn");
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tmp.add(r);
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tmp.add(rel(cc.getCcId(), id, "merges", dedupConf));
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tmp.add(rel(id, cc.getCcId(), "isMergedIn", dedupConf));
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return tmp.stream();
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}).iterator();
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}
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private Relation rel(String source, String target, String relClass, DedupConfig dedupConf) {
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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.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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public static long getHashcode(final String id) {
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return Hashing.murmur3_128().hashString(id).asLong();
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}
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@ -4,6 +4,7 @@ import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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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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@ -18,6 +19,7 @@ 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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@ -53,24 +55,27 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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final String actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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System.out.println(String.format("graphBasePath: '%s'", graphBasePath));
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System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl));
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System.out.println(String.format("actionSetId: '%s'", actionSetId));
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System.out.println(String.format("workingPath: '%s'", workingPath));
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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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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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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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System.out.println(String.format("Creating simrels for: '%s'", subEntity));
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log.info("Creating 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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JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
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.mapToPair((PairFunction<String, String, MapDocument>) s -> {
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MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
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return new Tuple2<String, MapDocument>(d.getIdentifier(), d);
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return new Tuple2<>(d.getIdentifier(), d);
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});
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//create blocks for deduplication
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@ -84,46 +89,30 @@ public class SparkCreateSimRels extends AbstractSparkAction {
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//save the simrel in the workingdir
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spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class))
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.write()
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.mode("overwrite")
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.save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity));
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.mode(SaveMode.Append)
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.save(outputPath);
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}
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}
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/**
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* Utility method used to create an atomic action from a Relation object
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* @param relation input relation
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* @return A tuple2 with [id, json serialization of the atomic action]
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* @throws JsonProcessingException
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*/
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public Tuple2<Text, Text> createSequenceFileRow(Relation relation) throws JsonProcessingException {
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ObjectMapper mapper = new ObjectMapper();
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String id = relation.getSource() + "@" + relation.getRelClass() + "@" + relation.getTarget();
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AtomicAction<Relation> aa = new AtomicAction<>(Relation.class, relation);
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return new Tuple2<>(
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new Text(id),
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new Text(mapper.writeValueAsString(aa))
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);
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}
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public Relation createSimRel(String source, String target, String entity){
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public Relation createSimRel(String source, String target, String entity) {
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final Relation r = new Relation();
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r.setSource(source);
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r.setTarget(target);
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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.setRelClass("resultResult_dedupSimilarity_isSimilarTo");
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r.setRelType("resultResult");
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break;
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case "organization":
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r.setRelClass("organizationOrganization_dedupSimilarity_isSimilarTo");
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r.setRelType("organizationOrganization");
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break;
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default:
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r.setRelClass("isSimilarTo");
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break;
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throw new IllegalArgumentException("unmanaged entity type: " + entity);
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}
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return r;
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}
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}
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@ -27,9 +27,6 @@ public class SparkPropagateRelation extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkPropagateRelation.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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enum FieldType {
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SOURCE,
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TARGET
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@ -62,7 +59,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
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log.info("dedupGraphPath: '{}'", dedupGraphPath);
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final String outputRelationPath = DedupUtility.createEntityPath(dedupGraphPath, "relation");
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deletePath(outputRelationPath);
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removeOutputDir(spark, outputRelationPath);
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Dataset<Relation> mergeRels = spark.read()
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.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
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@ -3,17 +3,18 @@ package eu.dnetlib.dhp.oa.dedup;
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import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.common.EntityType;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.*;
|
||||
import org.apache.hadoop.fs.FileStatus;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.hadoop.io.compress.GzipCodec;
|
||||
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;
|
||||
|
@ -27,7 +28,7 @@ import org.slf4j.LoggerFactory;
|
|||
import scala.Tuple2;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.util.Map;
|
||||
|
||||
public class SparkUpdateEntity extends AbstractSparkAction {
|
||||
|
||||
|
@ -48,98 +49,87 @@ public class SparkUpdateEntity extends AbstractSparkAction {
|
|||
new SparkUpdateEntity(parser, getSparkSession(parser)).run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
|
||||
}
|
||||
|
||||
public boolean mergeRelExists(String basePath, String entity) throws IOException {
|
||||
|
||||
boolean result = false;
|
||||
|
||||
FileSystem fileSystem = FileSystem.get(new Configuration());
|
||||
|
||||
FileStatus[] fileStatuses = fileSystem.listStatus(new Path(basePath));
|
||||
|
||||
for (FileStatus fs : fileStatuses) {
|
||||
if (fs.isDirectory())
|
||||
if (fileSystem.exists(new Path(DedupUtility.createMergeRelPath(basePath, fs.getPath().getName(), entity))))
|
||||
result = true;
|
||||
}
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
public void run(ISLookUpService isLookUpService) throws IOException {
|
||||
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
final String workingPath = parser.get("workingPath");
|
||||
final String dedupGraphPath = parser.get("dedupGraphPath");
|
||||
|
||||
System.out.println(String.format("graphBasePath: '%s'", graphBasePath));
|
||||
System.out.println(String.format("workingPath: '%s'", workingPath));
|
||||
System.out.println(String.format("dedupGraphPath: '%s'", dedupGraphPath));
|
||||
log.info("graphBasePath: '{}'", graphBasePath);
|
||||
log.info("workingPath: '{}'", workingPath);
|
||||
log.info("dedupGraphPath: '{}'", dedupGraphPath);
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
//for each entity
|
||||
for (OafEntityType entity: OafEntityType.values()) {
|
||||
ModelSupport.entityTypes.forEach((entity, clazz) -> {
|
||||
final String outputPath = dedupGraphPath + "/" + entity;
|
||||
removeOutputDir(spark, outputPath);
|
||||
|
||||
JavaRDD<String> sourceEntity = sc.textFile(DedupUtility.createEntityPath(graphBasePath, entity.toString()));
|
||||
|
||||
if (mergeRelExists(workingPath, entity.toString())) {
|
||||
|
||||
final Dataset<Relation> rel = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", entity.toString())).as(Encoders.bean(Relation.class));
|
||||
final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, "*", entity.toString());
|
||||
final String dedupRecordPath = DedupUtility.createDedupRecordPath(workingPath, "*", entity.toString());
|
||||
|
||||
final Dataset<Relation> rel = spark.read()
|
||||
.load(mergeRelPath)
|
||||
.as(Encoders.bean(Relation.class));
|
||||
|
||||
final JavaPairRDD<String, String> mergedIds = rel
|
||||
.where("relClass == 'merges'")
|
||||
.select(rel.col("target"))
|
||||
.distinct()
|
||||
.toJavaRDD()
|
||||
.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
|
||||
.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
|
||||
|
||||
final JavaRDD<String> dedupEntity = sc.textFile(DedupUtility.createDedupRecordPath(workingPath, "*", entity.toString()));
|
||||
JavaPairRDD<String, String> entitiesWithId = sourceEntity
|
||||
.mapToPair((PairFunction<String, String, String>) s -> new Tuple2<>(MapDocumentUtil.getJPathString(IDJSONPATH, s), s));
|
||||
|
||||
JavaPairRDD<String, String> entitiesWithId = sourceEntity.mapToPair((PairFunction<String, String, String>) s -> new Tuple2<String, String>(MapDocumentUtil.getJPathString(IDJSONPATH, s), s));
|
||||
|
||||
JavaRDD<String> map = entitiesWithId.leftOuterJoin(mergedIds).map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), getOafClass(entity)) : k._2()._1());
|
||||
sourceEntity = map.union(dedupEntity);
|
||||
JavaRDD<String> map = entitiesWithId
|
||||
.leftOuterJoin(mergedIds)
|
||||
.map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), clazz) : k._2()._1());
|
||||
|
||||
sourceEntity = map.union(sc.textFile(dedupRecordPath));
|
||||
}
|
||||
|
||||
sourceEntity.saveAsTextFile(dedupGraphPath + "/" + entity, GzipCodec.class);
|
||||
sourceEntity.saveAsTextFile(outputPath, GzipCodec.class);
|
||||
|
||||
}
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
public Class<? extends Oaf> getOafClass(OafEntityType className) {
|
||||
switch (className.toString()) {
|
||||
case "publication":
|
||||
return Publication.class;
|
||||
case "dataset":
|
||||
return eu.dnetlib.dhp.schema.oaf.Dataset.class;
|
||||
case "datasource":
|
||||
return Datasource.class;
|
||||
case "software":
|
||||
return Software.class;
|
||||
case "organization":
|
||||
return Organization.class;
|
||||
case "otherresearchproduct":
|
||||
return OtherResearchProduct.class;
|
||||
case "project":
|
||||
return Project.class;
|
||||
default:
|
||||
throw new IllegalArgumentException("Illegal type " + className);
|
||||
}
|
||||
}
|
||||
public boolean mergeRelExists(String basePath, String entity) {
|
||||
|
||||
private static <T extends Oaf> String updateDeletedByInference(final String json, final Class<T> clazz) {
|
||||
final ObjectMapper mapper = new ObjectMapper();
|
||||
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
boolean result = false;
|
||||
try {
|
||||
Oaf entity = mapper.readValue(json, clazz);
|
||||
FileSystem fileSystem = FileSystem.get(new Configuration());
|
||||
|
||||
FileStatus[] fileStatuses = fileSystem.listStatus(new Path(basePath));
|
||||
|
||||
for (FileStatus fs : fileStatuses) {
|
||||
if (fs.isDirectory())
|
||||
if (fileSystem.exists(new Path(DedupUtility.createMergeRelPath(basePath, fs.getPath().getName(), entity))))
|
||||
result = true;
|
||||
}
|
||||
|
||||
return result;
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private static <T extends OafEntity> String updateDeletedByInference(final String json, final Class<T> clazz) {
|
||||
try {
|
||||
Oaf entity = OBJECT_MAPPER.readValue(json, clazz);
|
||||
if (entity.getDataInfo()== null)
|
||||
entity.setDataInfo(new DataInfo());
|
||||
entity.getDataInfo().setDeletedbyinference(true);
|
||||
return mapper.writeValueAsString(entity);
|
||||
return OBJECT_MAPPER.writeValueAsString(entity);
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException("Unable to convert json", e);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -68,38 +68,12 @@
|
|||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="UpdateEntity"/>
|
||||
<start to="PropagateRelation"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="UpdateEntity">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Update Entity</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.SparkUpdateEntity</class>
|
||||
<jar>dhp-dedup-openaire-${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>-mt</arg><arg>yarn</arg>
|
||||
<arg>--i</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--w</arg><arg>${workingPath}</arg>
|
||||
<arg>--o</arg><arg>${dedupGraphPath}</arg>
|
||||
</spark>
|
||||
<ok to="PropagateRelation"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="PropagateRelation">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
@ -122,9 +96,112 @@
|
|||
<arg>--o</arg><arg>${dedupGraphPath}</arg>
|
||||
<arg>--w</arg><arg>${workingPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<ok to="fork_copy_entities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="fork_copy_entities">
|
||||
<path start="copy_datasource"/>
|
||||
<path start="copy_project"/>
|
||||
<path start="copy_organization"/>
|
||||
<path start="copy_publication"/>
|
||||
<path start="copy_dataset"/>
|
||||
<path start="copy_software"/>
|
||||
<path start="copy_otherresearchproduct"/>
|
||||
</fork>
|
||||
|
||||
<action name="copy_datasource">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/datasource"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/datasource</arg>
|
||||
<arg>${dedupGraphPath}/datasource</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_project">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/project"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/project</arg>
|
||||
<arg>${dedupGraphPath}/project</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/organization"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/organization</arg>
|
||||
<arg>${dedupGraphPath}/organization</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_publication">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/publication"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/publication</arg>
|
||||
<arg>${dedupGraphPath}/publication</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_dataset">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/dataset"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/dataset</arg>
|
||||
<arg>${dedupGraphPath}/dataset</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_software">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/software"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/software</arg>
|
||||
<arg>${dedupGraphPath}/software</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_otherresearchproduct">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/otherresearchproduct"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/otherresearchproduct</arg>
|
||||
<arg>${dedupGraphPath}/otherresearchproduct</arg>
|
||||
</distcp>
|
||||
<ok to="wait_copy"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait_copy" to="End"/>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
|
@ -16,6 +16,10 @@
|
|||
<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>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
|
@ -146,6 +150,7 @@
|
|||
--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>-mt</arg><arg>yarn</arg>
|
||||
<arg>--i</arg><arg>${graphBasePath}</arg>
|
||||
|
@ -153,6 +158,45 @@
|
|||
<arg>--la</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--asi</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>-mt</arg><arg>yarn</arg>
|
||||
<arg>--i</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--w</arg><arg>${workingPath}</arg>
|
||||
<arg>--o</arg><arg>${dedupGraphPath}</arg>
|
||||
</spark>
|
||||
<ok to="copyRelations"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copyRelations">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<prepare>
|
||||
<delete path="${dedupGraphPath}/relation"/>
|
||||
</prepare>
|
||||
<arg>-pb</arg>
|
||||
<arg>${graphBasePath}/relation</arg>
|
||||
<arg>${dedupGraphPath}/relation</arg>
|
||||
</distcp>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
|
Loading…
Reference in New Issue