[raw_all] added extra workflow step for patching the identifiers in the relations, given an id mapping dataset
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package eu.dnetlib.dhp.oa.graph.raw;
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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.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
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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.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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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 scala.Tuple2;
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import java.io.FileNotFoundException;
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import java.util.Objects;
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import java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class PatchRelationsApplication {
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private static final Logger log = LoggerFactory.getLogger(PatchRelationsApplication.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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Optional.ofNullable(
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PatchRelationsApplication.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/patch_relations_parameters.json"))
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.orElseThrow(FileNotFoundException::new)
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));
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parser.parseArgument(args);
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final 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 graphBasePath = parser.get("graphBasePath");
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log.info("graphBasePath: {}", graphBasePath);
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final String workingDir = parser.get("workingDir");
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log.info("workingDir: {}", workingDir);
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final String idMappingPath = parser.get("idMappingPath");
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log.info("idMappingPath: {}", idMappingPath);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> patchRelations(spark, graphBasePath, workingDir, idMappingPath));
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}
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/**
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* Substitutes the identifiers (source/target) from the set of relations part of the graphBasePath included in the
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* mapping provided by the dataset stored on idMappingPath, using workingDir as intermediate storage location.
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*
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* @param spark the SparkSession
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* @param graphBasePath base graph path providing the set of relations to patch
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* @param workingDir intermediate storage location
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* @param idMappingPath dataset providing the old -> new identifier mapping
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*/
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private static void patchRelations(final SparkSession spark, final String graphBasePath, final String workingDir, final String idMappingPath) {
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final String relationPath = graphBasePath + "/relation";
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final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
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final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
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rels
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.joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
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.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
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final Relation r = t._1();
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Optional.ofNullable(t._2())
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.map(RelationIdMapping::getNewId)
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.ifPresent(r::setSource);
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return r;
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}, Encoders.bean(Relation.class))
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.joinWith(idMapping, rels.col("target").equalTo(idMapping.col("oldId")), "left")
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.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {
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final Relation r = t._1();
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Optional.ofNullable(t._2())
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.map(RelationIdMapping::getNewId)
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.ifPresent(r::setTarget);
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return r;
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}, Encoders.bean(Relation.class))
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.map(
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(MapFunction<Relation, String>) OBJECT_MAPPER::writeValueAsString,
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Encoders.STRING())
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(workingDir);
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spark.read().textFile(workingDir)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(relationPath);
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}
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}
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@ -0,0 +1,24 @@
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package eu.dnetlib.dhp.oa.graph.raw.common;
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public class RelationIdMapping {
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private String oldId;
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private String newId;
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public String getOldId() {
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return oldId;
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}
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public void setOldId(final String oldId) {
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this.oldId = oldId;
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}
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public String getNewId() {
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return newId;
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}
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public void setNewId(final String newId) {
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this.newId = newId;
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}
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}
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@ -0,0 +1,26 @@
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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": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "g",
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"paramLongName": "graphBasePath",
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"paramDescription": "base graph path providing the set of relations to patch",
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"paramRequired": true
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},
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{
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"paramName": "w",
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"paramLongName": "workingDir",
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"paramDescription": "intermediate storage location",
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"paramRequired": true
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},
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{
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"paramName": "i",
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"paramLongName": "idMappingPath",
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"paramDescription": "dataset providing the old -> new identifier mapping",
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"paramRequired": true
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}
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]
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@ -100,6 +100,16 @@
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<value></value>
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<description>a blacklist of nsprefixes (comma separeted)</description>
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</property>
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<property>
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<name>shouldPatchRelations</name>
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<value>false</value>
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<description>activates the relation patching phase, driven by the content in ${idMappingPath}</description>
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</property>
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<property>
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<name>idMappingPath</name>
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<value></value>
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<description>path pointing to the relations identifiers mapping dataset</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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@ -538,7 +548,42 @@
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<error to="Kill"/>
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</action>
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<join name="wait_graphs" to="fork_merge_claims"/>
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<join name="wait_graphs" to="patchRelations"/>
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<decision name="decisionPatchRelations">
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<switch>
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<case to="patchRelations">
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${(shouldPatchRelations eq "true") and
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(fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")}
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</case>
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<default to="fork_merge_claims"/>
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</switch>
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</decision>
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<action name="patchRelations">
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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>PatchRelations</name>
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<class>eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication</class>
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<jar>dhp-graph-mapper-${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}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--graphBasePath</arg><arg>${workingDir}/graph_raw</arg>
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<arg>--workingDir</arg><arg>${workingDir}/patch_relations</arg>
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<arg>--idMappingPath</arg><arg>${idMappingPath}</arg>
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</spark>
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<ok to="fork_merge_claims"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_merge_claims">
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<path start="merge_claims_publication"/>
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