forked from antonis.lempesis/dnet-hadoop
updated generate scholix to generate json
This commit is contained in:
parent
0594b92a6d
commit
a768226e52
|
|
@ -4,6 +4,7 @@
|
|||
*.ipr
|
||||
*.iml
|
||||
*~
|
||||
.vscode
|
||||
.classpath
|
||||
/*/.classpath
|
||||
/*/*/.classpath
|
||||
|
|
|
|||
|
|
@ -1,55 +1,30 @@
|
|||
package eu.dnetlib.dhp.provision;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.provision.scholix.*;
|
||||
import eu.dnetlib.dhp.provision.scholix.summary.*;
|
||||
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
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.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FlatMapFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.PairFlatMapFunction;
|
||||
import org.apache.spark.sql.*;
|
||||
|
||||
import static org.apache.spark.sql.functions.col;
|
||||
|
||||
import scala.Int;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Random;
|
||||
|
||||
public class SparkGenerateScholix {
|
||||
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateScholix.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("spark.sql.shuffle.partitions","4000");
|
||||
// conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
// conf.registerKryoClasses(new Class[]{
|
||||
// ScholixSummary.class,
|
||||
// CollectedFromType.class,
|
||||
// SchemeValue.class,
|
||||
// TypedIdentifier.class,
|
||||
// Typology.class,
|
||||
// Relation.class,
|
||||
// Scholix.class,
|
||||
// ScholixCollectedFrom.class,
|
||||
// ScholixEntityId.class,
|
||||
// ScholixIdentifier.class,
|
||||
// ScholixRelationship.class,
|
||||
// ScholixResource.class
|
||||
// });
|
||||
|
||||
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
final SparkSession spark = SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
|
|
@ -57,6 +32,16 @@ public class SparkGenerateScholix {
|
|||
.master(parser.get("master"))
|
||||
.getOrCreate();
|
||||
|
||||
conf.registerKryoClasses(new Class[]{
|
||||
Scholix.class,
|
||||
ScholixCollectedFrom.class,
|
||||
ScholixEntityId.class,
|
||||
ScholixIdentifier.class,
|
||||
ScholixRelationship.class,
|
||||
ScholixResource.class
|
||||
});
|
||||
|
||||
|
||||
|
||||
final String graphPath = parser.get("graphPath");
|
||||
final String workingDirPath = parser.get("workingDirPath");
|
||||
|
|
@ -71,12 +56,16 @@ public class SparkGenerateScholix {
|
|||
.map((MapFunction<Tuple2<ScholixSummary, Relation>, Scholix>) f -> Scholix.generateScholixWithSource(f._1(), f._2()), Encoders.bean(Scholix.class));
|
||||
|
||||
firstJoin.write().mode(SaveMode.Overwrite).save(workingDirPath+"/scholix_1");
|
||||
firstJoin = spark.read().load(workingDirPath+"/scholix_1").as(Encoders.bean(Scholix.class));
|
||||
|
||||
|
||||
|
||||
Dataset<Scholix> scholix_final = spark.read().load(workingDirPath+"/scholix_1").as(Encoders.bean(Scholix.class));
|
||||
|
||||
scholixSummary
|
||||
.map((MapFunction<ScholixSummary, ScholixResource>) ScholixResource::fromSummary, Encoders.bean(ScholixResource.class))
|
||||
.repartition(1000)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(workingDirPath+"/scholix_target");
|
||||
|
||||
Dataset<ScholixResource> target = spark.read().load(workingDirPath+"/scholix_target").as(Encoders.bean(ScholixResource.class));
|
||||
|
||||
scholix_final.joinWith(target, scholix_final.col("identifier").equalTo(target.col("dnetIdentifier")), "inner")
|
||||
|
|
@ -87,6 +76,9 @@ public class SparkGenerateScholix {
|
|||
scholix.generateIdentifier();
|
||||
scholix.generatelinkPublisher();
|
||||
return scholix;
|
||||
}, Encoders.bean(Scholix.class)).repartition(5000).write().mode(SaveMode.Overwrite).save(workingDirPath+"/scholix_index");
|
||||
}, Encoders.kryo(Scholix.class)).javaRDD().map(s-> {
|
||||
ObjectMapper mapper = new ObjectMapper();
|
||||
return mapper.writeValueAsString(s);
|
||||
}).saveAsTextFile(workingDirPath+"/scholix_json", GzipCodec.class);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -33,11 +33,9 @@
|
|||
<name>idSummary</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
|
||||
|
||||
</parameters>
|
||||
|
||||
<start to="indexScholix"/>
|
||||
<start to="indexSummary"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
|
|
@ -96,12 +94,12 @@
|
|||
<name>generate Scholix</name>
|
||||
<class>eu.dnetlib.dhp.provision.SparkGenerateScholix</class>
|
||||
<jar>dhp-graph-provision-${projectVersion}.jar</jar>
|
||||
<spark-opts>--executor-memory 9G --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
|
||||
<spark-opts>--executor-memory 6G --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
|
||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||
<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
|
||||
<arg>--graphPath</arg><arg>${graphPath}</arg>
|
||||
</spark>
|
||||
<ok to="indexScholix"/>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
|
@ -111,7 +109,7 @@
|
|||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>generate Summary</name>
|
||||
<name>index Summary</name>
|
||||
<class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
|
||||
<jar>dhp-graph-provision-${projectVersion}.jar</jar>
|
||||
<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="64" </spark-opts>
|
||||
|
|
@ -134,7 +132,7 @@
|
|||
<name>index scholix</name>
|
||||
<class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
|
||||
<jar>dhp-graph-provision-${projectVersion}.jar</jar>
|
||||
<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="16" </spark-opts>
|
||||
<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" </spark-opts>
|
||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${workingDirPath}/scholix_json</arg>
|
||||
<arg>--index</arg><arg>${index}_scholix</arg>
|
||||
|
|
|
|||
Loading…
Reference in New Issue