added possibility to copy the graph from hive
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package eu.dnetlib.dhp.oa.graph.dump;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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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.FlatMapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import scala.Tuple2;
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/**
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* @author miriam.baglioni
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* @Date 22/09/23
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*/
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public class SparkCopyGraph implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkCopyGraph.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SparkCopyGraph.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/copygraph_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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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 hivePath = parser.get("hivePath");
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log.info("hivePath: {}", hivePath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark ->
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execCopy(
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spark,
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hivePath,
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outputPath));
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}
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private static void execCopy(SparkSession spark, String hivePath, String outputPath) {
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ModelSupport.oafTypes.entrySet().parallelStream().forEach(entry -> {
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String entityType = entry.getKey();
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Class<?> clazz = entry.getValue();
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// if (!entityType.equalsIgnoreCase("relation")) {
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spark
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.read()
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.schema(Encoders.bean(clazz).schema())
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.parquet(hivePath + "/" + entityType)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/" + entityType);
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});
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}
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}
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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>hiveMetastoreUris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>hiveJdbcUrl</name>
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<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
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</property>
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<property>
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<name>hiveDbName</name>
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<value>openaire</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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<workflow-app name="copy_graph_from_hive" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>outputPath</name>
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<description>the output path</description>
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</property>
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<property>
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<name>hivePath</name>
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<description>the country for which to produce the dump</description>
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</property>
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<property>
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<name>hiveDbName</name>
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<description>the target hive database name</description>
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</property>
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<property>
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<name>hiveJdbcUrl</name>
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<description>hive server jdbc url</description>
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</property>
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<property>
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<name>hiveMetastoreUris</name>
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<description>hive server metastore URIs</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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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</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>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="copy_graph" />
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<!-- <start to="make_archive" />-->
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="copy_graph">
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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>Copy graph</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.SparkCopyGraph</class>
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<jar>dump-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${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}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--hivePath</arg><arg>${hivePath}</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End" />
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</workflow-app>
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@ -0,0 +1,21 @@
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[
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{
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"paramName": "out",
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"paramLongName": "outputPath",
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"paramDescription": "the path used to store temporary output files",
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"paramRequired": true
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},
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{
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"paramName":"hp",
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"paramLongName":"hivePath",
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"paramDescription": "the name of the result table we are currently working on",
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"paramRequired": true
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},
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{
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"paramName":"issm",
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"paramLongName":"isSparkSessionManaged",
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"paramDescription": "the name of the result table we are currently working on",
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"paramRequired": false
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}
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]
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<error to="Kill"/>
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</action>
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<decision name="choose_dump">
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<switch>
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<case to="dump_funder">${wf:conf('dumpType') eq "funder"}</case>
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