forked from D-Net/dnet-hadoop
grouping graph entities by id turned out to be an easy extension for the already existing cleaning workflow
This commit is contained in:
parent
2bed29eb09
commit
528231a287
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@ -6,7 +6,9 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.Optional;
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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.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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@ -69,12 +71,12 @@ public class CleanGraphSparkJob {
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conf,
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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fixGraphTable(spark, vocs, inputPath, entityClazz, outputPath);
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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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cleanGraphTable(spark, vocs, inputPath, entityClazz, outputPath);
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});
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}
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private static <T extends Oaf> void fixGraphTable(
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private static <T extends Oaf> void cleanGraphTable(
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SparkSession spark,
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VocabularyGroup vocs,
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String inputPath,
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@ -100,13 +102,15 @@ public class CleanGraphSparkJob {
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return spark
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.read()
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.textFile(inputEntityPath)
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.filter((FilterFunction<String>) s -> isEntityType(s, clazz))
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.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
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.map(
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(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
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Encoders.bean(clazz));
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}
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private static void removeOutputDir(SparkSession spark, String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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private static <T extends Oaf> boolean isEntityType(final String s, final Class<T> clazz) {
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return StringUtils.substringBefore(s, "|").equals(clazz.getName());
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}
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}
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.oa.graph.groupbyid;
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package eu.dnetlib.dhp.oa.graph.clean;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
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@ -1,97 +0,0 @@
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package eu.dnetlib.dhp.oa.graph.groupbyid;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.Optional;
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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.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import scala.Tuple2;
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public class DispatchEntitiesSparkJob {
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private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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MigrateMongoMdstoresApplication.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dispatch_entities_bytype_parameters.json")));
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String entitiesPath = parser.get("entitiesPath");
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log.info("entitiesPath: {}", entitiesPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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dispatchOaf(spark, entityClazz, entitiesPath, outputPath);
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});
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}
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private static <T extends Oaf> void dispatchOaf(
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final SparkSession spark,
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final Class<T> clazz,
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final String sourcePath,
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final String targetPath) {
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log.info("Processing entities ({}) in file: {}", clazz.getName(), sourcePath);
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spark
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.read()
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.textFile(sourcePath)
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.filter((FilterFunction<String>) s -> isEntityType(s, clazz))
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.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.text(targetPath);
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}
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private static <T extends Oaf> boolean isEntityType(final String s, final Class<T> clazz) {
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return StringUtils.substringBefore(s, "|").equals(clazz.getName());
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}
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}
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@ -50,12 +50,36 @@
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</property>
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</parameters>
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<start to="fork_clean_graph"/>
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<start to="group_entities"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="group_entities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>group graph entities and relations</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.GroupEntitiesAndRelationsSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--graphInputPath</arg><arg>${graphInputPath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/grouped_entities</arg>
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</spark>
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<ok to="fork_clean_graph"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_clean_graph">
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<path start="clean_publication"/>
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<path start="clean_dataset"/>
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@ -1,18 +0,0 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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</configuration>
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@ -1,293 +0,0 @@
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<workflow-app name="group graph entities and relations" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>graphInputPath</name>
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<description>the graph root input path</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the graph root output path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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<description>spark 2.* extra listeners classname</description>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</description>
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</property>
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</parameters>
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<start to="group_entities"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="group_entities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>group graph entities and relations</name>
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<class>eu.dnetlib.dhp.oa.graph.groupbyid.GroupEntitiesAndRelationsSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--graphInputPath</arg><arg>${graphInputPath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/grouped_entities</arg>
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</spark>
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<ok to="fork_dispatch_entities"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_dispatch_entities">
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<path start="dispatch_publication"/>
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<path start="dispatch_dataset"/>
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<path start="dispatch_software"/>
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<path start="dispatch_otherresearchproduct"/>
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<path start="dispatch_datasource"/>
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<path start="dispatch_organization"/>
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<path start="dispatch_project"/>
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<path start="dispatch_relation"/>
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</fork>
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<action name="dispatch_publication">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch publications</name>
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<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_dataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch datasets</name>
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<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_software">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch softwares</name>
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<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${outputPath}/software</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_otherresearchproduct">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch otherresearchproducts</name>
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<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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</action>
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<action name="dispatch_datasource">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dispatch datasources</name>
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<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
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<arg>--outputPath</arg><arg>${outputPath}/datasource</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
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</spark>
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<ok to="wait_dispatch"/>
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<error to="Kill"/>
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||||
</action>
|
||||
|
||||
<action name="dispatch_organization">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch organizations</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/organization</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_project">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch project</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/project</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="dispatch_relation">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Dispatch relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.groupbyid.DispatchEntitiesSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--entitiesPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
|
||||
</spark>
|
||||
<ok to="wait_dispatch"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait_dispatch" to="End"/>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
Loading…
Reference in New Issue