implementation of the workflow for entity update and for relations update

This commit is contained in:
miconis 2020-03-20 13:01:56 +01:00
parent 6d879e2ee1
commit e16e644faf
15 changed files with 809 additions and 366 deletions

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@ -122,6 +122,10 @@ public class DedupUtility {
}); });
} }
public static String createDedupRecordPath(final String basePath, final String actionSetId, final String entityType) {
return String.format("%s/%s/%s_deduprecord", basePath, actionSetId, entityType);
}
public static String createEntityPath(final String basePath, final String entityType) { public static String createEntityPath(final String basePath, final String entityType) {
return String.format("%s/%s", basePath, entityType); return String.format("%s/%s", basePath, entityType);
} }

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@ -5,9 +5,11 @@ import eu.dnetlib.dedup.graph.ConnectedComponent;
import eu.dnetlib.dedup.graph.GraphProcessor; import eu.dnetlib.dedup.graph.GraphProcessor;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.util.MapDocumentUtil; import eu.dnetlib.pace.util.MapDocumentUtil;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
@ -18,6 +20,7 @@ import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import scala.Tuple2; import scala.Tuple2;
import java.util.ArrayList; import java.util.ArrayList;
@ -26,51 +29,72 @@ import java.util.List;
public class SparkCreateConnectedComponent { public class SparkCreateConnectedComponent {
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/createSimRels_parameters.json"))); final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/createCC_parameters.json")));
parser.parseArgument(args); parser.parseArgument(args);
final SparkSession spark = SparkSession
.builder()
.appName(SparkCreateConnectedComponent.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); new SparkCreateConnectedComponent().run(parser);
final String inputPath = parser.get("sourcePath"); }
final String entity = parser.get("entity");
final String targetPath = parser.get("targetPath");
// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json")));
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
final JavaPairRDD<Object, String> vertexes = sc.textFile(inputPath + "/" + entity) private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException {
.map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s))
.mapToPair((PairFunction<String, Object, String>)
s -> new Tuple2<Object, String>(getHashcode(s), s)
);
final Dataset<Relation> similarityRelations = spark.read().load(DedupUtility.createSimRelPath(targetPath, "",entity)).as(Encoders.bean(Relation.class)); final String graphBasePath = parser.get("graphBasePath");
final RDD<Edge<String>> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd(); final String workingPath = parser.get("workingPath");
final JavaRDD<ConnectedComponent> cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD(); final String isLookUpUrl = parser.get("isLookUpUrl");
final Dataset<Relation> mergeRelation = spark.createDataset(cc.filter(k->k.getDocIds().size()>1).flatMap((FlatMapFunction<ConnectedComponent, Relation>) c -> final String actionSetId = parser.get("actionSetId");
c.getDocIds()
.stream() try (SparkSession spark = getSparkSession(parser)) {
.flatMap(id -> {
List<Relation> tmp = new ArrayList<>(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
Relation r = new Relation();
r.setSource(c.getCcId()); for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) {
r.setTarget(id);
r.setRelClass("merges"); final String entity = dedupConf.getWf().getEntityType();
tmp.add(r); final String subEntity = dedupConf.getWf().getSubEntityValue();
r = new Relation();
r.setTarget(c.getCcId()); final JavaPairRDD<Object, String> vertexes = sc.textFile(graphBasePath + "/" + subEntity)
r.setSource(id); .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s))
r.setRelClass("isMergedIn"); .mapToPair((PairFunction<String, Object, String>)
tmp.add(r); s -> new Tuple2<Object, String>(getHashcode(s), s)
return tmp.stream(); );
}).iterator()).rdd(), Encoders.bean(Relation.class));
mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(targetPath,"",entity)); final Dataset<Relation> similarityRelations = spark.read().load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class));
final RDD<Edge<String>> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd();
final JavaRDD<ConnectedComponent> cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD();
final Dataset<Relation> mergeRelation = spark.createDataset(cc.filter(k -> k.getDocIds().size() > 1).flatMap((FlatMapFunction<ConnectedComponent, Relation>) c ->
c.getDocIds()
.stream()
.flatMap(id -> {
List<Relation> tmp = new ArrayList<>();
Relation r = new Relation();
r.setSource(c.getCcId());
r.setTarget(id);
r.setRelClass("merges");
tmp.add(r);
r = new Relation();
r.setTarget(c.getCcId());
r.setSource(id);
r.setRelClass("isMergedIn");
tmp.add(r);
return tmp.stream();
}).iterator()).rdd(), Encoders.bean(Relation.class));
mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(workingPath, actionSetId, entity));
}
}
} }
public static long getHashcode(final String id) { public static long getHashcode(final String id) {
return Hashing.murmur3_128().hashUnencodedChars(id).asLong(); return Hashing.murmur3_128().hashUnencodedChars(id).asLong();
} }
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
return SparkSession
.builder()
.appName(SparkCreateSimRels.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
}
} }

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@ -1,100 +0,0 @@
package eu.dnetlib.dedup;
import com.google.common.hash.Hashing;
import eu.dnetlib.dedup.graph.ConnectedComponent;
import eu.dnetlib.dedup.graph.GraphProcessor;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.util.MapDocumentUtil;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.graphx.Edge;
import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import scala.Tuple2;
import java.util.ArrayList;
import java.util.List;
public class SparkCreateConnectedComponent2 {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/createCC_parameters.json")));
parser.parseArgument(args);
new SparkCreateConnectedComponent2().run(parser);
}
private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException {
final String graphBasePath = parser.get("graphBasePath");
final String workingPath = parser.get("workingPath");
final String isLookUpUrl = parser.get("isLookUpUrl");
final String actionSetId = parser.get("actionSetId");
try (SparkSession spark = getSparkSession(parser)) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) {
final String entity = dedupConf.getWf().getEntityType();
final String subEntity = dedupConf.getWf().getSubEntityValue();
final JavaPairRDD<Object, String> vertexes = sc.textFile(graphBasePath + "/" + subEntity)
.map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s))
.mapToPair((PairFunction<String, Object, String>)
s -> new Tuple2<Object, String>(getHashcode(s), s)
);
final Dataset<Relation> similarityRelations = spark.read().load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class));
final RDD<Edge<String>> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd();
final JavaRDD<ConnectedComponent> cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD();
final Dataset<Relation> mergeRelation = spark.createDataset(cc.filter(k -> k.getDocIds().size() > 1).flatMap((FlatMapFunction<ConnectedComponent, Relation>) c ->
c.getDocIds()
.stream()
.flatMap(id -> {
List<Relation> tmp = new ArrayList<>();
Relation r = new Relation();
r.setSource(c.getCcId());
r.setTarget(id);
r.setRelClass("merges");
tmp.add(r);
r = new Relation();
r.setTarget(c.getCcId());
r.setSource(id);
r.setRelClass("isMergedIn");
tmp.add(r);
return tmp.stream();
}).iterator()).rdd(), Encoders.bean(Relation.class));
mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(workingPath, actionSetId, entity));
}
}
}
public static long getHashcode(final String id) {
return Hashing.murmur3_128().hashUnencodedChars(id).asLong();
}
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
return SparkSession
.builder()
.appName(SparkCreateSimRels2.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
}
}

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@ -3,37 +3,57 @@ package eu.dnetlib.dedup;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.config.DedupConfig;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
public class SparkCreateDedupRecord { public class SparkCreateDedupRecord {
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/dedupRecord_parameters.json"))); final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/createDedupRecord_parameters.json")));
parser.parseArgument(args); parser.parseArgument(args);
final SparkSession spark = SparkSession
new SparkCreateDedupRecord().run(parser);
}
private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException {
final String graphBasePath = parser.get("graphBasePath");
final String isLookUpUrl = parser.get("isLookUpUrl");
final String actionSetId = parser.get("actionSetId");
final String workingPath = parser.get("workingPath");
try (SparkSession spark = getSparkSession(parser)) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) {
String subEntity = dedupConf.getWf().getSubEntityValue();
final JavaRDD<OafEntity> dedupRecord =
DedupRecordFactory.createDedupRecord(sc, spark, DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity), DedupUtility.createEntityPath(graphBasePath, subEntity), OafEntityType.valueOf(subEntity), dedupConf);
dedupRecord.map(r -> {
ObjectMapper mapper = new ObjectMapper();
return mapper.writeValueAsString(r);
}).saveAsTextFile(DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity));
}
}
}
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
return SparkSession
.builder() .builder()
.appName(SparkCreateDedupRecord.class.getSimpleName()) .appName(SparkCreateDedupRecord.class.getSimpleName())
.master(parser.get("master")) .master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate(); .getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final String sourcePath = parser.get("sourcePath");
final String entity = parser.get("entity");
final String dedupPath = parser.get("dedupPath");
// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json")));
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
final JavaRDD<OafEntity> dedupRecord = DedupRecordFactory.createDedupRecord(sc, spark, DedupUtility.createMergeRelPath(dedupPath,entity), DedupUtility.createEntityPath(sourcePath,entity), OafEntityType.valueOf(entity), dedupConf);
dedupRecord.map(r-> {
ObjectMapper mapper = new ObjectMapper();
return mapper.writeValueAsString(r);
}).saveAsTextFile(dedupPath+"/"+entity+"_dedup_record_json");
} }
} }

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@ -1,71 +1,135 @@
package eu.dnetlib.dedup; package eu.dnetlib.dedup;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.util.MapDocumentUtil; import eu.dnetlib.pace.util.MapDocumentUtil;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import scala.Tuple2; import scala.Tuple2;
import java.io.Serializable;
import java.util.List; import java.util.List;
public class SparkCreateSimRels implements Serializable {
/** private static final Log log = LogFactory.getLog(SparkCreateSimRels.class);
* This Spark class creates similarity relations between entities, saving result
*
* param request:
* sourcePath
* entityType
* target Path
*/
public class SparkCreateSimRels {
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/createSimRels_parameters.json"))); final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/createSimRels_parameters.json")));
parser.parseArgument(args); parser.parseArgument(args);
final SparkSession spark = SparkSession
new SparkCreateSimRels().run(parser);
}
private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException {
//read oozie parameters
final String graphBasePath = parser.get("graphBasePath");
final String rawSet = parser.get("rawSet");
final String isLookUpUrl = parser.get("isLookUpUrl");
final String actionSetId = parser.get("actionSetId");
final String workingPath = parser.get("workingPath");
try (SparkSession spark = getSparkSession(parser)) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
//create empty sequenceFile for the accumulation
JavaRDD<Tuple2<Text,Text>> simRel = sc.emptyRDD();
//for each dedup configuration
for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) {
final String entity = dedupConf.getWf().getEntityType();
final String subEntity = dedupConf.getWf().getSubEntityValue();
JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(graphBasePath + "/" + subEntity)
.mapToPair(s -> {
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
return new Tuple2<>(d.getIdentifier(), d);
});
//create blocks for deduplication
JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
//create relations by comparing only elements in the same group
final JavaPairRDD<String, String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
JavaRDD<Relation> relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity));
//save the simrel in the workingdir
spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)).write().mode("overwrite").save( DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity));
//create atomic actions
JavaRDD<Tuple2<Text, Text>> newSimRels = relationsRDD
.map(this::createSequenceFileRow);
simRel = simRel.union(newSimRels);
}
simRel.mapToPair(r -> r)
.saveAsHadoopFile(rawSet, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
}
}
public Tuple2<Text, Text> createSequenceFileRow(Relation relation) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
String id = relation.getSource() + "@" + relation.getRelClass() + "@" + relation.getTarget();
AtomicAction<Relation> aa = new AtomicAction<>(Relation.class, relation);
return new Tuple2<>(
new Text(id),
new Text(mapper.writeValueAsString(aa))
);
}
public Relation createSimRel(String source, String target, String entity){
final Relation r = new Relation();
r.setSource(source);
r.setTarget(target);
switch(entity){
case "result":
r.setRelClass("resultResult_dedupSimilarity_isSimilarTo");
break;
case "organization":
r.setRelClass("organizationOrganization_dedupSimilarity_isSimilarTo");
break;
default:
r.setRelClass("isSimilarTo");
break;
}
return r;
}
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
return SparkSession
.builder() .builder()
.appName(SparkCreateSimRels.class.getSimpleName()) .appName(SparkCreateSimRels.class.getSimpleName())
.master(parser.get("master")) .master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate(); .getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final String inputPath = parser.get("sourcePath");
final String entity = parser.get("entity");
final String targetPath = parser.get("targetPath");
// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
final long total = sc.textFile(inputPath + "/" + entity).count();
JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(inputPath + "/" + entity)
.mapToPair(s->{
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf,s);
return new Tuple2<>(d.getIdentifier(), d);});
//create blocks for deduplication
JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
// JavaPairRDD<String, Iterable<MapDocument>> blocks = Deduper.createBlocks(sc, mapDocument, dedupConf);
//create relations by comparing only elements in the same group
final JavaPairRDD<String,String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
// final JavaPairRDD<String,String> dedupRels = Deduper.computeRelations(sc, blocks, dedupConf);
final JavaRDD<Relation> isSimilarToRDD = dedupRels.map(simRel -> {
final Relation r = new Relation();
r.setSource(simRel._1());
r.setTarget(simRel._2());
r.setRelClass("isSimilarTo");
return r;
});
spark.createDataset(isSimilarToRDD.rdd(), Encoders.bean(Relation.class)).write().mode("overwrite").save( DedupUtility.createSimRelPath(targetPath,entity));
} }
} }

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@ -1,144 +0,0 @@
package eu.dnetlib.dedup;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.actionmanager.actions.AtomicAction;
import eu.dnetlib.actionmanager.common.Agent;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
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.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
import scala.Tuple2;
import java.io.Serializable;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
public class SparkCreateSimRels2 implements Serializable {
private static final Log log = LogFactory.getLog(SparkCreateSimRels2.class);
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/createSimRels_parameters.json")));
parser.parseArgument(args);
new SparkCreateSimRels2().run(parser);
}
private void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException {
//read oozie parameters
final String graphBasePath = parser.get("graphBasePath");
final String rawSet = parser.get("rawSet");
final String isLookUpUrl = parser.get("isLookUpUrl");
final String actionSetId = parser.get("actionSetId");
final String workingPath = parser.get("workingPath");
try (SparkSession spark = getSparkSession(parser)) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
//create empty sequenceFile for the accumulation
JavaRDD<Tuple2<Text,Text>> simRel = sc.emptyRDD();
//for each dedup configuration
for (DedupConfig dedupConf: DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) {
final String entity = dedupConf.getWf().getEntityType();
final String subEntity = dedupConf.getWf().getSubEntityValue();
JavaPairRDD<String, MapDocument> mapDocument = sc.textFile(graphBasePath + "/" + subEntity)
.mapToPair(s -> {
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
return new Tuple2<>(d.getIdentifier(), d);
});
//create blocks for deduplication
JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
//create relations by comparing only elements in the same group
final JavaPairRDD<String, String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
JavaRDD<Relation> relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2(), entity));
//save the simrel in the workingdir
spark.createDataset(relationsRDD.rdd(), Encoders.bean(Relation.class)).write().mode("overwrite").save( DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity));
//create atomic actions
JavaRDD<Tuple2<Text, Text>> newSimRels = relationsRDD
.map(this::createSequenceFileRow);
simRel = simRel.union(newSimRels);
}
simRel.mapToPair(r -> r)
.saveAsHadoopFile(rawSet, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
}
}
public Tuple2<Text, Text> createSequenceFileRow(Relation relation) throws JsonProcessingException {
ObjectMapper mapper = new ObjectMapper();
String id = relation.getSource() + "@" + relation.getRelClass() + "@" + relation.getTarget();
//TODO do be replaced by the new implementation of AtomicAction
AtomicAction aa = new AtomicAction("rawSet", new Agent("agentId", "agentName", Agent.AGENT_TYPE.service), relation.getSource(), relation.getRelClass(), relation.getTarget(), new ObjectMapper().writeValueAsString(relation).getBytes());
return new Tuple2<>(
new Text(id),
new Text(mapper.writeValueAsString(aa))
);
}
public Relation createSimRel(String source, String target, String entity){
final Relation r = new Relation();
r.setSource(source);
r.setTarget(target);
switch(entity){
case "result":
r.setRelClass("resultResult_dedupSimilarity_isSimilarTo");
break;
case "organization":
r.setRelClass("organizationOrganization_dedupSimilarity_isSimilarTo");
break;
default:
r.setRelClass("isSimilarTo");
break;
}
return r;
}
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
return SparkSession
.builder()
.appName(SparkCreateSimRels2.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
}
}

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@ -0,0 +1,169 @@
package eu.dnetlib.dedup;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.pace.util.MapDocumentUtil;
import org.apache.commons.io.IOUtils;
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;
import org.apache.spark.api.java.Optional;
import org.apache.spark.api.java.function.Function;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import scala.Tuple2;
import java.io.IOException;
public class SparkPropagateRelation {
enum FieldType {
SOURCE,
TARGET
}
final static String SOURCEJSONPATH = "$.source";
final static String TARGETJSONPATH = "$.target";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkPropagateRelation.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/propagateRelation_parameters.json")));
parser.parseArgument(args);
new SparkPropagateRelation().run(parser);
}
public void run(ArgumentApplicationParser parser) {
final String graphBasePath = parser.get("graphBasePath");
final String workingPath = parser.get("workingPath");
final String dedupGraphPath = parser.get("dedupGraphPath");
try (SparkSession spark = getSparkSession(parser)) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final Dataset<Relation> mergeRels = spark.read().load(DedupUtility.createMergeRelPath(workingPath, "*", "*")).as(Encoders.bean(Relation.class));
final JavaPairRDD<String, String> mergedIds = mergeRels
.where("relClass == 'merges'")
.select(mergeRels.col("source"), mergeRels.col("target"))
.distinct()
.toJavaRDD()
.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(1), r.getString(0)));
JavaRDD<String> relations = sc.textFile(DedupUtility.createEntityPath(graphBasePath, "relation"));
JavaRDD<String> newRels = relations.mapToPair(
(PairFunction<String, String, String>) s ->
new Tuple2<>(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s))
.leftOuterJoin(mergedIds)
.map((Function<Tuple2<String, Tuple2<String, Optional<String>>>, String>) v1 -> {
if (v1._2()._2().isPresent()) {
return replaceField(v1._2()._1(), v1._2()._2().get(), FieldType.SOURCE);
}
return v1._2()._1();
})
.mapToPair(
(PairFunction<String, String, String>) s ->
new Tuple2<>(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s))
.leftOuterJoin(mergedIds)
.map((Function<Tuple2<String, Tuple2<String, Optional<String>>>, String>) v1 -> {
if (v1._2()._2().isPresent()) {
return replaceField(v1._2()._1(), v1._2()._2().get(), FieldType.TARGET);
}
return v1._2()._1();
}).filter(SparkPropagateRelation::containsDedup)
.repartition(500);
//update deleted by inference
relations = relations.mapToPair(
(PairFunction<String, String, String>) s ->
new Tuple2<>(MapDocumentUtil.getJPathString(SOURCEJSONPATH, s), s))
.leftOuterJoin(mergedIds)
.map((Function<Tuple2<String, Tuple2<String, Optional<String>>>, String>) v1 -> {
if (v1._2()._2().isPresent()) {
return updateDeletedByInference(v1._2()._1(), Relation.class);
}
return v1._2()._1();
})
.mapToPair(
(PairFunction<String, String, String>) s ->
new Tuple2<>(MapDocumentUtil.getJPathString(TARGETJSONPATH, s), s))
.leftOuterJoin(mergedIds)
.map((Function<Tuple2<String, Tuple2<String, Optional<String>>>, String>) v1 -> {
if (v1._2()._2().isPresent()) {
return updateDeletedByInference(v1._2()._1(), Relation.class);
}
return v1._2()._1();
})
.repartition(500);
newRels.union(relations).repartition(1000)
.saveAsTextFile(DedupUtility.createEntityPath(dedupGraphPath, "relation"), GzipCodec.class);
}
}
private static boolean containsDedup(final String json) {
final String source = MapDocumentUtil.getJPathString(SOURCEJSONPATH, json);
final String target = MapDocumentUtil.getJPathString(TARGETJSONPATH, json);
return source.toLowerCase().contains("dedup") || target.toLowerCase().contains("dedup");
}
private static String replaceField(final String json, final String id, final FieldType type) {
ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
try {
Relation relation = mapper.readValue(json, Relation.class);
if (relation.getDataInfo() == null)
relation.setDataInfo(new DataInfo());
relation.getDataInfo().setDeletedbyinference(false);
switch (type) {
case SOURCE:
relation.setSource(id);
return mapper.writeValueAsString(relation);
case TARGET:
relation.setTarget(id);
return mapper.writeValueAsString(relation);
default:
throw new IllegalArgumentException("");
}
} catch (IOException e) {
throw new RuntimeException("unable to deserialize json relation: " + json, e);
}
}
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
return SparkSession
.builder()
.appName(SparkPropagateRelation.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
}
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);
try {
Oaf entity = mapper.readValue(json, clazz);
if (entity.getDataInfo()== null)
entity.setDataInfo(new DataInfo());
entity.getDataInfo().setDeletedbyinference(true);
return mapper.writeValueAsString(entity);
} catch (IOException e) {
throw new RuntimeException("Unable to convert json", e);
}
}
}

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@ -0,0 +1,121 @@
package eu.dnetlib.dedup;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.util.MapDocumentUtil;
import org.apache.commons.io.IOUtils;
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;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import scala.Tuple2;
import java.io.IOException;
public class SparkUpdateEntity {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkUpdateEntity.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/updateEntity_parameters.json")));
parser.parseArgument(args);
new SparkUpdateEntity().run(parser);
}
public void run(ArgumentApplicationParser parser) throws ISLookUpException, DocumentException {
final String graphBasePath = parser.get("graphBasePath");
final String workingPath = parser.get("workingPath");
final String dedupGraphPath = parser.get("dedupGraphPath");
final String isLookUpUrl = parser.get("isLookUpUrl");
final String actionSetId = parser.get("actionSetId");
try (SparkSession spark = getSparkSession(parser)) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
for (DedupConfig dedupConf : DedupUtility.getConfigurations(isLookUpUrl, actionSetId)) {
String subEntity = dedupConf.getWf().getSubEntityValue();
final Dataset<Relation> df = spark.read().load(DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity)).as(Encoders.bean(Relation.class));
final JavaPairRDD<String, String> mergedIds = df
.where("relClass == 'merges'")
.select(df.col("target"))
.distinct()
.toJavaRDD()
.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
final JavaRDD<String> sourceEntity = sc.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity));
final JavaRDD<String> dedupEntity = sc.textFile(DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity));
JavaPairRDD<String, String> entitiesWithId = sourceEntity.mapToPair((PairFunction<String, String, String>) s -> new Tuple2<>(MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s), s));
Class<? extends Oaf> mainClass;
switch (subEntity) {
case "publication":
mainClass = Publication.class;
break;
case "dataset":
mainClass = eu.dnetlib.dhp.schema.oaf.Dataset.class;
break;
case "datasource":
mainClass = Datasource.class;
break;
case "software":
mainClass = Software.class;
break;
case "organization":
mainClass = Organization.class;
break;
case "otherresearchproduct":
mainClass = OtherResearchProduct.class;
break;
default:
throw new IllegalArgumentException("Illegal type " + subEntity);
}
JavaRDD<String> map = entitiesWithId.leftOuterJoin(mergedIds).map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), mainClass) : k._2()._1());
map.union(dedupEntity).saveAsTextFile(dedupGraphPath + "/" + subEntity, GzipCodec.class);
}
}
}
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);
try {
Oaf entity = mapper.readValue(json, clazz);
if (entity.getDataInfo()== null)
entity.setDataInfo(new DataInfo());
entity.getDataInfo().setDeletedbyinference(true);
return mapper.writeValueAsString(entity);
} catch (IOException e) {
throw new RuntimeException("Unable to convert json", e);
}
}
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
SparkConf conf = new SparkConf();
return SparkSession
.builder()
.appName(SparkUpdateEntity.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
}
}

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@ -0,0 +1,32 @@
[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "graphBasePath",
"paramDescription": "the base path of raw graph",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "the working directory path",
"paramRequired": true
},
{
"paramName": "la",
"paramLongName": "isLookUpUrl",
"paramDescription": "the url of the lookup service",
"paramRequired": true
},
{
"paramName": "asi",
"paramLongName": "actionSetId",
"paramDescription": "the id of the actionset (orchestrator)",
"paramRequired": true
}
]

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@ -0,0 +1,129 @@
<workflow-app name="Build Root Records" 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 of the working directory</description>
</property>
<property>
<name>dedupGraphPath</name>
<description>path of the dedup graph</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>
</parameters>
<start to="DeleteWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DeleteWorkingPath">
<fs>
<delete path='${workingPath}/${actionSetId}/*_mergerel'/>
<delete path='${workingPath}/${actionSetId}/*_deduprecord'/>
</fs>
<ok to="CreateMergeRel"/>
<error to="Kill"/>
</action>
<action name="CreateMergeRel">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Merge Relations</name>
<class>eu.dnetlib.dedup.SparkCreateConnectedComponent</class>
<jar>dhp-dedup-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --conf
spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf
spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf
spark.sql.warehouse.dir="/user/hive/warehouse"
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--i</arg><arg>${graphBasePath}</arg>
<arg>--w</arg><arg>${workingPath}</arg>
<arg>--la</arg><arg>${isLookUpUrl}</arg>
<arg>--asi</arg><arg>${actionSetId}</arg>
</spark>
<ok to="CreateDedupRecord"/>
<error to="Kill"/>
</action>
<action name="CreateDedupRecord">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Dedup Record</name>
<class>eu.dnetlib.dedup.SparkCreateDedupRecord</class>
<jar>dhp-dedup-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --conf
spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf
spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf
spark.sql.warehouse.dir="/user/hive/warehouse"
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--i</arg><arg>${graphBasePath}</arg>
<arg>--w</arg><arg>${workingPath}</arg>
<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">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Dedup Record</name>
<class>eu.dnetlib.dedup.SparkUpdateEntity</class>
<jar>dhp-dedup-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --conf
spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf
spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf
spark.sql.warehouse.dir="/user/hive/warehouse"
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--i</arg><arg>${graphBasePath}</arg>
<arg>--w</arg><arg>${workingPath}</arg>
<arg>--la</arg><arg>${isLookUpUrl}</arg>
<arg>--asi</arg><arg>${actionSetId}</arg>
<arg>--o</arg><arg>${dedupGraphPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -55,7 +55,7 @@
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Create Similarity Relations</name> <name>Create Similarity Relations</name>
<class>eu.dnetlib.dedup.SparkCreateSimRels2</class> <class>eu.dnetlib.dedup.SparkCreateSimRels</class>
<jar>dhp-dedup-${projectVersion}.jar</jar> <jar>dhp-dedup-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} <spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --conf --driver-memory=${sparkDriverMemory} --conf
@ -64,10 +64,11 @@
spark.sql.warehouse.dir="/user/hive/warehouse" spark.sql.warehouse.dir="/user/hive/warehouse"
</spark-opts> </spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg> <arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--i</arg><arg>${rawGraphBasePath}</arg> <arg>--i</arg><arg>${graphBasePath}</arg>
<arg>--o</arg><arg>${rawSet}</arg> <arg>--o</arg><arg>${rawSet}</arg>
<arg>--la</arg><arg>${isLookUpUrl}</arg> <arg>--la</arg><arg>${isLookUpUrl}</arg>
<arg>--asi</arg><arg>${actionSetId}</arg> <arg>--asi</arg><arg>${actionSetId}</arg>
<arg>--w</arg><arg>${workingPath}</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>

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<workflow-app name="Create Similarity Relations" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>graphBasePath</name>
<description>the raw graph base path</description>
</property>
<property>
<name>workingPath</name>
<description>path for the working directory</description>
</property>
<property>
<name>dedupGraphPath</name>
<description>path of the dedup graph</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>
</parameters>
<start to="DeleteWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DeleteWorkingPath">
<fs>
<delete path='${dedupGraphPath}/relation'/>
</fs>
<ok to="DuplicateScan"/>
<error to="Kill"/>
</action>
<action name="DuplicateScan">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Update Relations</name>
<class>eu.dnetlib.dedup.SparkPropagateRelation</class>
<jar>dhp-dedup-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --conf
spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf
spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf
spark.sql.warehouse.dir="/user/hive/warehouse"
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--i</arg><arg>${graphBasePath}</arg>
<arg>--o</arg><arg>${dedupGraphPath}</arg>
<arg>--w</arg><arg>${workingPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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@ -0,0 +1,26 @@
[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "graphBasePath",
"paramDescription": "the base path of raw graph",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "the working directory path",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "dedupGraphPath",
"paramDescription": "the path of the dedup graph",
"paramRequired": true
}
]

View File

@ -0,0 +1,38 @@
[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "graphBasePath",
"paramDescription": "the base path of raw graph",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "the working directory path",
"paramRequired": true
},
{
"paramName": "la",
"paramLongName": "isLookUpUrl",
"paramDescriptions": "the url of the lookup service",
"paramRequired": true
},
{
"paramName": "asi",
"paramLongName": "actionSetId",
"paramDescriptions": "the id of the actionset (orchestrator)",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "dedupGraphPath",
"paramDescription": "the path of the dedup graph",
"paramRequired": true
}
]

View File

@ -1,21 +1,14 @@
package eu.dnetlib.dedup; package eu.dnetlib.dedup;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.hash.HashFunction; import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing; import com.google.common.hash.Hashing;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Publication;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.junit.Before; import org.junit.Before;
import org.junit.Ignore; import org.junit.Ignore;
import org.junit.Test; import org.junit.Test;
import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
public class SparkCreateDedupTest { public class SparkCreateDedupTest {
@ -27,22 +20,10 @@ public class SparkCreateDedupTest {
configuration = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dedup/conf/org.curr.conf.json")); configuration = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dedup/conf/org.curr.conf.json"));
} }
@Test
@Ignore
public void createSimRelsTest() throws Exception {
SparkCreateSimRels.main(new String[] {
"-mt", "local[*]",
"-s", "/Users/miconis/dumps",
"-e", entity,
"-c", ArgumentApplicationParser.compressArgument(configuration),
"-t", "/tmp/dedup",
});
}
@Test @Test
@Ignore @Ignore
public void createSimRelsTest2() throws Exception { public void createSimRelsTest2() throws Exception {
SparkCreateSimRels2.main(new String[] { SparkCreateSimRels.main(new String[] {
"-mt", "local[*]", "-mt", "local[*]",
"-s", "/Users/miconis/dumps", "-s", "/Users/miconis/dumps",
"-e", entity, "-e", entity,
@ -98,4 +79,14 @@ public class SparkCreateDedupTest {
System.out.println(hashFunction.hashUnencodedChars(s2).asLong()); System.out.println(hashFunction.hashUnencodedChars(s2).asLong());
} }
@Test
public void testJoinEntities() throws Exception{
SparkJoinEntities.main(new String[] {
"-mt", "local[*]",
"-i", "/tmp/dedup",
"-w", "/tmp/dedup",
"-o", "/tmp/dedup",
});
}
} }