forked from D-Net/dnet-hadoop
added script to download the dump,changed the workflow input paramenters
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83c04e5d28
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5faeefbda8
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@ -29,16 +29,16 @@ public class ExtractCrossrefRecords {
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"/eu/dnetlib/dhp/doiboost/crossref_dump_reader.json")));
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parser.parseArgument(args);
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final String hdfsServerUri = parser.get("hdfsServerUri");
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final String workingPath = parser.get("workingPath");
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final String workingPath = hdfsServerUri.concat(parser.get("workingPath"));
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final String outputPath = parser.get("outputPath");
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final String crossrefFileNameTarGz = parser.get("crossrefFileNameTarGz");
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Path hdfsreadpath = new Path(hdfsServerUri.concat(crossrefFileNameTarGz));
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Path hdfsreadpath = new Path(workingPath.concat("/").concat(crossrefFileNameTarGz));
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsServerUri.concat(workingPath));
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conf.set("fs.defaultFS", workingPath);
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conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
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conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
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FileSystem fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf);
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FileSystem fs = FileSystem.get(URI.create(workingPath), conf);
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FSDataInputStream crossrefFileStream = fs.open(hdfsreadpath);
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try (TarArchiveInputStream tais = new TarArchiveInputStream(
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new GzipCompressorInputStream(crossrefFileStream))) {
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@ -0,0 +1,2 @@
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#!/bin/bash
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curl -LSs -H "Crossref-Plus-API-Token: Bearer eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJodHRwOi8vY3Jvc3NyZWYub3JnLyIsImF1ZCI6Im1kcGx1cyIsImp0aSI6Ijk3YTZkNGVkLTg5MjktNGQ2Yi05NWY1LTY2YmMyNDgzNTRjNCJ9.5DPM4gRibUBYBtrUSpRz3RGHYVB-8f61jQBW_q-r-hs" $1 | hdfs dfs -put $2/$3
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@ -1,13 +1,5 @@
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<workflow-app name="read Crossref dump from HDFS" xmlns="uri:oozie:workflow:0.5">
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<workflow-app name="CROSSREF DUMP - DOWNLOAD" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>crossrefDumpPath</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>inputPathCrossref</name>
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<description>the working dir base 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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@ -18,27 +10,82 @@
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<value>2</value>
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<description>number of cores used by single executor</description>
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</property>
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<!-- Crossref Parameters -->
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<property>
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<name>crossrefdumpfilename</name>
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<description>the Crossref input path</description>
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</property>
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<property>
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<name>crossrefDumpPath</name>
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<description>the Crossref dump path</description>
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</property>
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</parameters>
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<start to="GenerateCrossrefDataset"/>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="ImportCrossRef"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="removeFiles">
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<fs>
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<delete path="${crossrefDumpPath}/${crossrefdumpfilename}"/>
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<delete path="${crossrefDumpPath}/files"/>
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<delete path="${crossrefDumpPath}/crossref_unpack"/>
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</fs>
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<ok to="DownloadDump"/>
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<error to="Kill"/>
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</action>
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<action name="DownloadDump">
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<shell xmlns="uri:oozie:shell-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapred.job.queue.name</name>
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<value>${queueName}</value>
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</property>
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</configuration>
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<exec>download.sh</exec>
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<argument>${url}</argument>
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<argument>${crossrefDumpPath}</argument>
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<argument>${crossrefdumpfilename}</argument>
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<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
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<file>download.sh</file>
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<capture-output/>
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</shell>
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<ok to="ImportCrossRef"/>
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<error to="Kill"/>
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</action>
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<action name="ImportCrossRef">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
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<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
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<arg>--crossrefFileNameTarGz</arg><arg>${crossrefDumpPath}/crossref.tar.gz</arg>
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<arg>--crossrefFileNameTarGz</arg><arg>${crossrefdumpfilename}</arg>
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<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/files/</arg>
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<arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
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</java>
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<ok to="UnpackCrossrefEntries"/>
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<error to="Kill"/>
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@ -48,7 +95,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>SparkGenerateCrossrefDataset</name>
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<name>SparkUnpackCrossrefEntries</name>
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<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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@ -63,56 +110,14 @@
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</spark-opts>
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<arg>--master</arg><arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
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</spark>
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<ok to="GenerateCrossrefDataset"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateCrossrefDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>SparkGenerateCrossrefDataset</name>
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<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
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<jar>dhp-doiboost-${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=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${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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</spark-opts>
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<arg>--master</arg><arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds_updates</arg>
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<arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<!-- <action name="removeFiles">-->
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<!-- <fs>-->
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<!-- <delete path="${workingDir}/files"/>-->
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<!-- </fs>-->
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<!-- <ok to="renameDataset"/>-->
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<!-- <error to="Kill"/>-->
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<!-- </action>-->
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<!-- <action name="renameDataset">-->
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<!-- <fs>-->
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<!-- <delete path="${inputPathCrossref}/crossref_ds"/>-->
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<!-- <move source="${inputPathCrossref}/crossref_ds_updated"-->
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<!-- target="${inputPathCrossref}/crossref_ds"/>-->
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<!-- </fs>-->
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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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