joining entities using T x R x S method with groupByKey

This commit is contained in:
Claudio Atzori 2020-01-21 16:35:44 +01:00
parent 1cd6899480
commit 799929c1e3
19 changed files with 238 additions and 500 deletions

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>eu.dnetlib.dhp</groupId> <groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId> <artifactId>dhp</artifactId>
<version>1.1.5-SNAPSHOT</version> <version>1.0.5-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>

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@ -1,118 +0,0 @@
package eu.dnetlib.dhp.schema.dli;
import java.io.Serializable;
import java.util.List;
public class Entity implements Serializable {
private String identifier;
private List<Pid> pid;
private List<String> title;
private List<String> date;
private String typology;
private List<String> authors;
private List<Subject> subject;
private String description;
private String completionStatus;
private List<Provenance> collectedFrom;
private List<String> publisher;
public String getIdentifier() {
return identifier;
}
public void setIdentifier(String identifier) {
this.identifier = identifier;
}
public List<Pid> getPid() {
return pid;
}
public void setPid(List<Pid> pid) {
this.pid = pid;
}
public List<String> getTitle() {
return title;
}
public void setTitle(List<String> title) {
this.title = title;
}
public List<String> getDate() {
return date;
}
public void setDate(List<String> date) {
this.date = date;
}
public String getTypology() {
return typology;
}
public void setTypology(String typology) {
this.typology = typology;
}
public List<String> getAuthors() {
return authors;
}
public void setAuthors(List<String> authors) {
this.authors = authors;
}
public List<Subject> getSubject() {
return subject;
}
public void setSubject(List<Subject> subject) {
this.subject = subject;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
public List<Provenance> getCollectedFrom() {
return collectedFrom;
}
public void setCollectedFrom(List<Provenance> collectedFrom) {
this.collectedFrom = collectedFrom;
}
public List<String> getPublisher() {
return publisher;
}
public void setPublisher(List<String> publisher) {
this.publisher = publisher;
}
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
}

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@ -1,33 +0,0 @@
package eu.dnetlib.dhp.schema.dli;
import eu.dnetlib.dhp.utils.DHPUtils;
import org.apache.commons.lang3.StringUtils;
public class Pid {
private String pid;
private String pidType;
public String getPid() {
return pid;
}
public void setPid(String pid) {
this.pid = pid;
}
public String getPidType() {
return pidType;
}
public void setPidType(String pidType) {
this.pidType = pidType;
}
public String generateId() {
if(StringUtils.isEmpty(pid) || StringUtils.isEmpty(pidType))
return null;
return DHPUtils.md5(String.format("%s::%s", pid, pidType));
}
}

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@ -1,35 +0,0 @@
package eu.dnetlib.dhp.schema.dli;
public class Provenance {
private String datasourceId;
private String datasourceName;
private String completionStatus;
public String getDatasourceId() {
return datasourceId;
}
public void setDatasourceId(String datasourceId) {
this.datasourceId = datasourceId;
}
public String getDatasourceName() {
return datasourceName;
}
public void setDatasourceName(String datasourceName) {
this.datasourceName = datasourceName;
}
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
}

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@ -1,47 +0,0 @@
package eu.dnetlib.dhp.schema.dli;
import java.io.Serializable;
import java.util.List;
public class Relation implements Serializable {
private String source;
private String target;
private List<Provenance> provenance;
private RelationSemantic semantic;
public String getSource() {
return source;
}
public void setSource(String source) {
this.source = source;
}
public String getTarget() {
return target;
}
public void setTarget(String target) {
this.target = target;
}
public List<Provenance> getProvenance() {
return provenance;
}
public void setProvenance(List<Provenance> provenance) {
this.provenance = provenance;
}
public RelationSemantic getSemantic() {
return semantic;
}
public void setSemantic(RelationSemantic semantic) {
this.semantic = semantic;
}
}

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@ -1,16 +0,0 @@
package eu.dnetlib.dhp.schema.dli;
import java.io.Serializable;
public class RelationSemantic extends Subject implements Serializable {
public String inverse;
public String getInverse() {
return inverse;
}
public void setInverse(String inverse) {
this.inverse = inverse;
}
}

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@ -1,35 +0,0 @@
package eu.dnetlib.dhp.schema.dli;
import java.io.Serializable;
public class Subject implements Serializable {
private String schema;
private String value;
public Subject() {
}
public Subject(String schema, String value) {
this.schema = schema;
this.value = value;
}
public String getSchema() {
return schema;
}
public void setSchema(String schema) {
this.schema = schema;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

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@ -1,5 +1,4 @@
sparkDriverMemory=7G sparkDriverMemory=7G
sparkExecutorMemory=7G sparkExecutorMemory=7G
sparkExecutorMemoryOverhead=5G
hive_db_name=claudio hive_db_name=claudio
sourcePath=/tmp/db_openaireplus_services_beta.export.2019.11.06 sourcePath=/tmp/db_openaireplus_services_beta.export.2019.11.06

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@ -19,6 +19,10 @@
<groupId>org.apache.spark</groupId> <groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId> <artifactId>spark-sql_2.11</artifactId>
</dependency> </dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
</dependency>
<dependency> <dependency>
<groupId>eu.dnetlib.dhp</groupId> <groupId>eu.dnetlib.dhp</groupId>

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@ -1,4 +0,0 @@
package eu.dnetlib.dhp.graph;
public class EntityNode {
}

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@ -1,20 +1,30 @@
package eu.dnetlib.dhp.graph; package eu.dnetlib.dhp.graph;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.io.Serializable; import java.io.Serializable;
public class EntityRelEntity implements Serializable { public class EntityRelEntity implements Serializable {
private TypedRow source; private TypedRow source;
private Relation relation; private TypedRow relation;
private TypedRow target; private TypedRow target;
public EntityRelEntity() {
}
public EntityRelEntity(TypedRow source) { public EntityRelEntity(TypedRow source) {
this.source = source; this.source = source;
} }
//helpers
public Boolean hasMainEntity() {
return getSource() != null & getRelation() == null & getTarget() == null;
}
public Boolean hasRelatedEntity() {
return getSource() == null & getRelation() != null & getTarget() != null;
}
public TypedRow getSource() { public TypedRow getSource() {
return source; return source;
} }
@ -24,11 +34,11 @@ public class EntityRelEntity implements Serializable {
return this; return this;
} }
public Relation getRelation() { public TypedRow getRelation() {
return relation; return relation;
} }
public EntityRelEntity setRelation(Relation relation) { public EntityRelEntity setRelation(TypedRow relation) {
this.relation = relation; this.relation = relation;
return this; return this;
} }
@ -42,12 +52,4 @@ public class EntityRelEntity implements Serializable {
return this; return this;
} }
@Override
public String toString() {
try {
return new ObjectMapper().writeValueAsString(this);
} catch (JsonProcessingException e) {
throw new RuntimeException(e);
}
}
} }

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@ -1,139 +1,119 @@
package eu.dnetlib.dhp.graph; package eu.dnetlib.dhp.graph;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.*; import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;
import com.jayway.jsonpath.JsonPath;
import org.apache.hadoop.io.Text; import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
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.api.java.Optional;
import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import scala.Tuple2; import scala.Tuple2;
import java.io.Serializable; import java.io.Serializable;
import java.util.List;
public class GraphJoiner implements Serializable { public class GraphJoiner implements Serializable {
public static final int MAX_RELS = 100; public static final int MAX_RELS = 10;
public void join(final SparkSession spark, final String inputPath, final String hiveDbName, final String outPath) { public void join(final SparkSession spark, final String inputPath, final String hiveDbName, final String outPath) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
/* final String entityIdPath = "$.id";
JavaPairRDD<String, TypedRow> entities = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class))
.map(oaf -> new TypedRow("publication", oaf))
.mapToPair(toPair());
*/ JavaPairRDD<String, TypedRow> datasource = readPathEntity(sc, entityIdPath, inputPath, "datasource");
JavaPairRDD<String, TypedRow> organization = readPathEntity(sc, entityIdPath, inputPath, "organization");
JavaPairRDD<String, TypedRow> project = readPathEntity(sc, entityIdPath, inputPath, "project");
JavaPairRDD<String, TypedRow> dataset = readPathEntity(sc, entityIdPath, inputPath, "dataset");
JavaPairRDD<String, TypedRow> otherresearchproduct = readPathEntity(sc, entityIdPath, inputPath, "otherresearchproduct");
JavaPairRDD<String, TypedRow> software = readPathEntity(sc, entityIdPath, inputPath, "software");
JavaPairRDD<String, TypedRow> publication = readPathEntity(sc, entityIdPath, inputPath, "publication");
JavaPairRDD<String, TypedRow> entities = sc.sequenceFile(inputPath + "/datasource", Text.class, Text.class) final String entitiesPath = outPath + "/entities";
.map(item -> new ObjectMapper().readValue(item._2().toString(), Datasource.class)) datasource
.map(oaf -> new TypedRow("datasource", oaf)) .union(organization)
.mapToPair(toPair()) .union(project)
.union(sc.sequenceFile(inputPath + "/organization", Text.class, Text.class) .union(dataset)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Organization.class)) .union(otherresearchproduct)
.map(oaf -> new TypedRow("organization", oaf)) .union(software)
.mapToPair(toPair())) .union(publication)
.union(sc.sequenceFile(inputPath + "/project", Text.class, Text.class) .map(e -> new EntityRelEntity().setSource(e._2()))
.map(item -> new ObjectMapper().readValue(item._2().toString(), Project.class)) .map(e -> new ObjectMapper().writeValueAsString(e))
.map(oaf -> new TypedRow("project", oaf)) .saveAsTextFile(entitiesPath, GzipCodec.class);
.mapToPair(toPair()))
.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class))
.map(oaf -> new TypedRow("dataset", oaf))
.mapToPair(toPair()))
.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class))
.map(oaf -> new TypedRow("otherresearchproduct", oaf))
.mapToPair(toPair()))
.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class))
.map(oaf -> new TypedRow("software", oaf))
.mapToPair(toPair()));
/*
.union(sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class))
.map(oaf -> new TypedRow("publication", oaf))
.mapToPair(toPair()));
*/ JavaPairRDD<String, EntityRelEntity> entities = sc.textFile(entitiesPath)
.map(t -> new ObjectMapper().readValue(t, EntityRelEntity.class))
.mapToPair(t -> new Tuple2<>(t.getSource().getSource(), t));
/* final JavaPairRDD<String, EntityRelEntity> relation = readPathRelation(sc, inputPath)
JavaRDD<Relation> rels = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class) .map(p -> new EntityRelEntity().setRelation(p))
.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class)) .mapToPair(p -> new Tuple2<>(p.getRelation().getSource(), p))
.map(oaf -> new TypedRow("relation", oaf))
.mapToPair(toPair())
.groupByKey() .groupByKey()
.map(t -> Iterables.limit(t._2(), MAX_RELS)) .map(p -> Iterables.limit(p._2(), MAX_RELS))
.flatMap(t -> t.iterator()) .flatMap(p -> p.iterator())
.map(t -> (Relation) t.getOaf()); .mapToPair(p -> new Tuple2<>(p.getRelation().getTarget(), p));
spark.createDataset(rels.rdd(), Encoders.bean(Relation.class)) final String joinByTargetPath = outPath + "/join_by_target";
.write() relation.join(entities)
.mode(SaveMode.Overwrite) .map(s -> new EntityRelEntity()
.saveAsTable(hiveDbName + ".relation_100"); .setRelation(s._2()._1().getRelation())
*/ .setTarget(s._2()._2().getSource()))
.map(e -> new ObjectMapper().writeValueAsString(e))
.saveAsTextFile(joinByTargetPath, GzipCodec.class);
JavaPairRDD<String, TypedRow> bounded_rels = spark.table(hiveDbName + ".relation_" + MAX_RELS)
.as(Encoders.bean(Relation.class))
.javaRDD()
.map(r -> new TypedRow("relation", r))
.mapToPair(toPair());
// build the adjacency list: e -> r JavaPairRDD<String, EntityRelEntity> bySource = sc.textFile(joinByTargetPath)
JavaPairRDD<String, Tuple2<TypedRow, Optional<TypedRow>>> adjacency_list = entities.leftOuterJoin(bounded_rels); .map(t -> new ObjectMapper().readValue(t, EntityRelEntity.class))
.mapToPair(t -> new Tuple2<>(t.getRelation().getSource(), t));
JavaRDD<EntityRelEntity> linked_entities = adjacency_list entities
.mapToPair(toPairTarget()) // make rel.targetid explicit so that we can join it .union(bySource)
.leftOuterJoin(entities) // again with the entities to get the target entity .groupByKey() // by source id
.map(l -> toEntityRelEntity(l)); // and map it to a more readable representation .map(p -> {
final LinkedEntity e = new LinkedEntity();
spark.createDataFrame(linked_entities, EntityRelEntity.class) final List<Tuple> links = Lists.newArrayList();
.write() for(EntityRelEntity rel : p._2()) {
.mode(SaveMode.Overwrite) if (rel.hasMainEntity() & e.getEntity() == null) {
.saveAsTable(hiveDbName + ".linked_entities"); e.setEntity(rel.getSource());
}
if (rel.hasRelatedEntity()) {
links.add(new Tuple()
.setRelation(rel.getRelation())
.setTarget(rel.getTarget()));
}
}
e.setLinks(links);
if (e.getEntity() == null) {
throw new IllegalStateException("missing main entity on '" + p._1() + "'");
}
return e;
})
.map(e -> new ObjectMapper().writeValueAsString(e))
.saveAsTextFile(outPath + "/linked_entities", GzipCodec.class);
} }
private EntityRelEntity toEntityRelEntity(Tuple2<String, Tuple2<Tuple2<String, Tuple2<TypedRow, Optional<TypedRow>>>, Optional<TypedRow>>> l) { private JavaPairRDD<String, TypedRow> readPathEntity(final JavaSparkContext sc, final String idPath, final String inputPath, final String type) {
// extract the entity source return sc.sequenceFile(inputPath + "/" + type, Text.class, Text.class)
final EntityRelEntity res = new EntityRelEntity(l._2()._1()._2()._1()); .mapToPair((PairFunction<Tuple2<Text, Text>, String, TypedRow>) item -> {
final String json = item._2().toString();
if(l._2()._1()._2()._2().isPresent() && l._2()._2().isPresent()) { final String id = JsonPath.read(json, idPath);
return new Tuple2<>(id, new TypedRow(id, type, json));
// extract the relationship });
res.setRelation((Relation) l._2()._1()._2()._2().get().getOaf());
// extract the related entity
res.setTarget(l._2()._2().get());
}
return res;
} }
private PairFunction<Tuple2<String, Tuple2<TypedRow, Optional<TypedRow>>>, String, Tuple2<String, Tuple2<TypedRow, Optional<TypedRow>>>> toPairTarget() { private JavaRDD<TypedRow> readPathRelation(final JavaSparkContext sc, final String inputPath) {
return e -> { return sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
Optional<TypedRow> o = e._2()._2(); .map(item -> {
if (o.isPresent()) { final String json = item._2().toString();
return new Tuple2<>(((Relation) o.get().getOaf()).getTarget(), e); final String source = JsonPath.read(json, "$.source");
} else { final String target = JsonPath.read(json, "$.target");
return new Tuple2<>(null, e); return new TypedRow(source, target, "relation", json);
} });
};
}
private PairFunction<TypedRow, String, TypedRow> toPair() {
return e -> {
if (!"relation".equals(e.getType())) {
return new Tuple2<>( ((OafEntity) e.getOaf()).getId(), e);
} else {
return new Tuple2<>( ((Relation) e.getOaf()).getSource(), e);
}
};
} }
} }

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@ -0,0 +1,29 @@
package eu.dnetlib.dhp.graph;
import java.io.Serializable;
import java.util.List;
public class LinkedEntity implements Serializable {
private TypedRow entity;
private List<Tuple> links;
public TypedRow getEntity() {
return entity;
}
public LinkedEntity setEntity(TypedRow entity) {
this.entity = entity;
return this;
}
public List<Tuple> getLinks() {
return links;
}
public LinkedEntity setLinks(List<Tuple> links) {
this.links = links;
return this;
}
}

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@ -1,69 +0,0 @@
package eu.dnetlib.dhp.graph;
import java.io.Serializable;
public class RelatedEntity implements Serializable {
private String relType;
private String subRelType;
private String relClass;
private String type;
private String payload;
public RelatedEntity(String relType, String subRelType, String relClass, String type, String payload) {
this.relType = relType;
this.subRelType = subRelType;
this.relClass = relClass;
this.type = type;
this.payload = payload;
}
public String getRelType() {
return relType;
}
public RelatedEntity setRelType(String relType) {
this.relType = relType;
return this;
}
public String getSubRelType() {
return subRelType;
}
public RelatedEntity setSubRelType(String subRelType) {
this.subRelType = subRelType;
return this;
}
public String getRelClass() {
return relClass;
}
public RelatedEntity setRelClass(String relClass) {
this.relClass = relClass;
return this;
}
public String getType() {
return type;
}
public RelatedEntity setType(String type) {
this.type = type;
return this;
}
public String getPayload() {
return payload;
}
public RelatedEntity setPayload(String payload) {
this.payload = payload;
return this;
}
}

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@ -4,21 +4,27 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path; import org.apache.hadoop.fs.Path;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
public class SparkGraphIndexingJob { public class SparkGraphIndexingJob {
private final static String ENTITY_NODES_PATH = "/tmp/entity_node"; private final static String OUTPUT_BASE_PATH = "/tmp/openaire_provision";
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGraphIndexingJob.class.getResourceAsStream("/eu/dnetlib/dhp/graph/input_graph_parameters.json"))); final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGraphIndexingJob.class.getResourceAsStream("/eu/dnetlib/dhp/graph/input_graph_parameters.json")));
parser.parseArgument(args); parser.parseArgument(args);
final SparkConf conf = new SparkConf()
.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
final SparkSession spark = SparkSession final SparkSession spark = SparkSession
.builder() .builder()
.config(conf)
.appName(SparkGraphIndexingJob.class.getSimpleName()) .appName(SparkGraphIndexingJob.class.getSimpleName())
.master(parser.get("master")) .master(parser.get("master"))
.config("hive.metastore.uris", parser.get("hive_metastore_uris"))
.enableHiveSupport() .enableHiveSupport()
.getOrCreate(); .getOrCreate();
@ -26,11 +32,12 @@ public class SparkGraphIndexingJob {
final String hiveDbName = parser.get("hive_db_name"); final String hiveDbName = parser.get("hive_db_name");
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
if (fs.exists(new Path(ENTITY_NODES_PATH))) { if (fs.exists(new Path(OUTPUT_BASE_PATH))) {
fs.delete(new Path(ENTITY_NODES_PATH), true); fs.delete(new Path(OUTPUT_BASE_PATH), true);
fs.mkdirs(new Path(OUTPUT_BASE_PATH));
} }
new GraphJoiner().join(spark, inputPath, hiveDbName, ENTITY_NODES_PATH); new GraphJoiner().join(spark, inputPath, hiveDbName, OUTPUT_BASE_PATH);
} }
} }

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@ -0,0 +1,31 @@
package eu.dnetlib.dhp.graph;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.io.Serializable;
public class Tuple implements Serializable {
private TypedRow relation;
private TypedRow target;
public TypedRow getRelation() {
return relation;
}
public Tuple setRelation(TypedRow relation) {
this.relation = relation;
return this;
}
public TypedRow getTarget() {
return target;
}
public Tuple setTarget(TypedRow target) {
this.target = target;
return this;
}
}

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@ -1,20 +1,46 @@
package eu.dnetlib.dhp.graph; package eu.dnetlib.dhp.graph;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import java.io.Serializable; import java.io.Serializable;
public class TypedRow implements Serializable { public class TypedRow implements Serializable {
private String type;
private Oaf oaf;
public TypedRow(String type, Oaf oaf) { private String source;
private String target;
private String type;
private String oaf;
public TypedRow() {
}
public TypedRow(String source, String type, String oaf) {
this.source = source;
this.type = type; this.type = type;
this.oaf = oaf; this.oaf = oaf;
} }
public TypedRow(String source, String target, String type, String oaf) {
this(source, type, oaf);
this.target = target;
}
public String getSource() {
return source;
}
public TypedRow setSource(String source) {
this.source = source;
return this;
}
public String getTarget() {
return target;
}
public TypedRow setTarget(String target) {
this.target = target;
return this;
}
public String getType() { public String getType() {
return type; return type;
} }
@ -24,21 +50,13 @@ public class TypedRow implements Serializable {
return this; return this;
} }
public Oaf getOaf() { public String getOaf() {
return oaf; return oaf;
} }
public TypedRow setOaf(Oaf oaf) { public TypedRow setOaf(String oaf) {
this.oaf = oaf; this.oaf = oaf;
return this; return this;
} }
@Override
public String toString() {
try {
return new ObjectMapper().writeValueAsString(this);
} catch (JsonProcessingException e) {
throw new RuntimeException(e);
}
}
} }

View File

@ -23,4 +23,12 @@
<name>hive_db_name</name> <name>hive_db_name</name>
<value>openaire</value> <value>openaire</value>
</property> </property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18088</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/applicationHistory</value>
</property>
</configuration> </configuration>

View File

@ -16,6 +16,14 @@
<name>sparkExecutorCores</name> <name>sparkExecutorCores</name>
<description>number of cores used by single executor</description> <description>number of cores used by single executor</description>
</property> </property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters> </parameters>
<start to="GraphJoinEntities"/> <start to="GraphJoinEntities"/>
@ -33,7 +41,16 @@
<name>GraphIndexing</name> <name>GraphIndexing</name>
<class>eu.dnetlib.dhp.graph.SparkGraphIndexingJob</class> <class>eu.dnetlib.dhp.graph.SparkGraphIndexingJob</class>
<jar>dhp-graph-provision-${projectVersion}.jar</jar> <jar>dhp-graph-provision-${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" --conf spark.yarn.executor.memoryOverhead=${sparkExecutorMemoryOverhead}</spark-opts> <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"
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg> <arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg> <arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_db_name</arg><arg>${hive_db_name}</arg> <arg>--hive_db_name</arg><arg>${hive_db_name}</arg>