forked from D-Net/dnet-hadoop
implementation and configuration for propagation of project to result through semantic relation: P -> R1 and R1 -> supplemented by -> R2 => P -> R2
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package eu.dnetlib.dhp.projecttoresult;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.TypedRow;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.SparkSession;
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import scala.Tuple2;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashSet;
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import java.util.List;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.PropagationConstant.toPair;
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public class SparkResultToProjectThroughSemRelJob {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToProjectThroughSemRelJob.class.getResourceAsStream("/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json")));
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parser.parseArgument(args);
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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkResultToProjectThroughSemRelJob.class.getSimpleName())
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.master(parser.get("master"))
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.enableHiveSupport()
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.getOrCreate();
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final String inputPath = parser.get("sourcePath");
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final String outputPath = "/tmp/provision/propagation/projecttoresult";
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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File directory = new File(outputPath);
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if (!directory.exists()) {
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directory.mkdirs();
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}
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JavaRDD<Relation> relations = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
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.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class)).cache();
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JavaPairRDD<String, TypedRow> result_result = relations
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.filter(r -> !r.getDataInfo().getDeletedbyinference())
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.filter(r -> allowedsemrel.contains(r.getRelClass()) && RELATION_RESULTRESULT_REL_TYPE.equals(r.getRelType()))
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.map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
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.mapToPair(toPair());
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JavaPairRDD<String, TypedRow> result_project = relations
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.filter(r -> !r.getDataInfo().getDeletedbyinference())
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.filter(r -> RELATION_RESULT_PROJECT_REL_CLASS.equals(r.getRelClass()) && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType()))
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.map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
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.mapToPair(toPair());
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//relationships from project to result. One pair for each relationship for results having allowed semantics relation with another result
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JavaPairRDD<String, TypedRow> project_result = result_project.join(result_result)
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.map(c -> {
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String projectId = c._2()._1().getTargetId();
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String resultId = c._2()._2().getTargetId();
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return new TypedRow().setSourceId(projectId).setTargetId(resultId);
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})
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.mapToPair(toPair());
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//relationships from project to result. One Pair for each project => project id list of results related to the project
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JavaPairRDD<String, TypedRow> project_results = relations
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.filter(r -> !r.getDataInfo().getDeletedbyinference())
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.filter(r -> RELATION_PROJECT_RESULT_REL_CLASS.equals(r.getRelClass()) && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType()))
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.map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
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.mapToPair(toPair())
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.reduceByKey((a, b) -> {
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if (a == null) {
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return b;
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}
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if (b == null) {
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return a;
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}
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a.addAll(b.getAccumulator());
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return a;
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});
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JavaRDD<Relation> newRels = project_result.join(project_results)
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.flatMap(c -> {
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String resId = c._2()._1().getTargetId();
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if (c._2()._2().getAccumulator().contains(resId)) {
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return null;
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}
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String progId = c._2()._1().getSourceId();
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List<Relation> rels = new ArrayList();
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rels.add(getRelation(progId, resId, RELATION_PROJECT_RESULT_REL_CLASS,
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RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
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rels.add(getRelation(resId, progId, RELATION_RESULT_PROJECT_REL_CLASS,
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RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
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return rels.iterator();
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})
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.cache();
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newRels.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath + "/relation_new");
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newRels.union(relations).map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath + "/relation");
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}
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}
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[
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{
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"paramName":"mt",
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"paramLongName":"master",
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"paramDescription": "should be local or yarn",
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"paramRequired": true
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},
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{
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"paramName":"s",
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"paramLongName":"sourcePath",
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"paramDescription": "the path of the sequencial file to read",
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"paramRequired": true
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},
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{
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"paramName":"asr",
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"paramLongName":"allowedsemrels",
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"paramDescription": "the types of the allowed datasources. Split by ;",
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"paramRequired": true
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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>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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<workflow-app name="project_to_result_propagation" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the source path</description>
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</property>
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<property>
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<name>allowedsemrels</name>
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<description>the allowed semantics </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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</parameters>
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<start to="ProjectPropagation"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ProjectPropagation">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ProjectToResultPropagation</name>
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<class>eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>--executor-memory ${sparkExecutorMemory}
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--executor-cores ${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
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--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
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</spark-opts>
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<arg>-mt</arg> <arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--allowedsemrels</arg><arg>${allowedsemrels}</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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