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