collecting all the atoic actions for result type and save them all in the AS path
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package eu.dnetlib.dhp.actionmanager.bipfinder;
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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.Optional;
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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.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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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.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.schema.oaf.Result;
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public class CollectAndSave implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static <I extends Result> void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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CollectAndSave.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.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 inputPath = parser.get("inputPath");
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log.info("inputPath {}: ", inputPath);
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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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removeOutputDir(spark, outputPath);
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collectAndSave(spark, inputPath, outputPath);
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});
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}
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private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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sc
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.sequenceFile(inputPath + "/publication", Text.class, Text.class)
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.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class))
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.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class))
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.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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;
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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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}
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}
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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": "ip",
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"paramLongName": "inputPath",
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"paramDescription": "the URL from where to get the programme file",
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"paramRequired": true
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},
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{
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"paramName": "o",
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"paramLongName": "outputPath",
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"paramDescription": "the path of the new ActionSet",
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"paramRequired": true
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},
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{
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"paramName": "rtn",
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"paramLongName": "resultTableName",
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"paramDescription": "the path of the new ActionSet",
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"paramRequired": true
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},
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{
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"paramName": "bsp",
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"paramLongName": "bipScorePath",
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"paramDescription": "the path of the new ActionSet",
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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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<property>
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<name>hive_metastore_uris</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>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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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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</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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</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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<property>
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<name>sparkExecutorNumber</name>
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<value>4</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<value>15G</value>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<value>6G</value>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<value>1</value>
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</property>
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</configuration>
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<workflow-app name="H2020Programme" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>projectFileURL</name>
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<description>the url where to get the projects file</description>
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</property>
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<property>
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<name>programmeFileURL</name>
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<description>the url where to get the programme file</description>
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</property>
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<property>
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<name>topicFileURL</name>
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<description>the url where to get the topic file</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>path where to store the action set</description>
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</property>
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</parameters>
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<start to="deleteoutputpath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="deleteoutputpath">
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<fs>
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<delete path='${outputPath}'/>
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<mkdir path='${outputPath}'/>
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<delete path='${workingDir}'/>
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<mkdir path='${workingDir}'/>
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</fs>
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<ok to="get_project_file"/>
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<error to="Kill"/>
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</action>
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<action name="get_project_file">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--fileURL</arg><arg>${projectFileURL}</arg>
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<arg>--hdfsPath</arg><arg>${workingDir}/projects</arg>
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<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.project.utils.CSVProject</arg>
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</java>
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<ok to="get_programme_file"/>
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<error to="Kill"/>
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</action>
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<action name="get_programme_file">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--fileURL</arg><arg>${programmeFileURL}</arg>
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<arg>--hdfsPath</arg><arg>${workingDir}/programme</arg>
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<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme</arg>
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</java>
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<ok to="get_topic_file"/>
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<error to="Kill"/>
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</action>
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<action name="get_topic_file">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadExcel</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--fileURL</arg><arg>${topicFileURL}</arg>
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<arg>--hdfsPath</arg><arg>${workingDir}/topic</arg>
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<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.project.utils.EXCELTopic</arg>
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</java>
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<ok to="read_projects"/>
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<error to="Kill"/>
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</action>
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<action name="read_projects">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.project.ReadProjectsFromDB</main-class>
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<arg>--hdfsPath</arg><arg>${workingDir}/dbProjects</arg>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
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<arg>--postgresUser</arg><arg>${postgresUser}</arg>
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<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
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</java>
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<ok to="prepare_programme"/>
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<error to="Kill"/>
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</action>
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<action name="prepare_programme">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>PrepareProgramme</name>
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<class>eu.dnetlib.dhp.actionmanager.project.PrepareProgramme</class>
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<jar>dhp-aggregation-${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=3840
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</spark-opts>
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<arg>--programmePath</arg><arg>${workingDir}/programme</arg>
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<arg>--outputPath</arg><arg>${workingDir}/preparedProgramme</arg>
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</spark>
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<ok to="prepare_project"/>
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<error to="Kill"/>
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</action>
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<action name="prepare_project">
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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>PrepareProjects</name>
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<class>eu.dnetlib.dhp.actionmanager.project.PrepareProjects</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${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}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=3840
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</spark-opts>
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<arg>--projectPath</arg><arg>${workingDir}/projects</arg>
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<arg>--outputPath</arg><arg>${workingDir}/preparedProjects</arg>
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<arg>--dbProjectPath</arg><arg>${workingDir}/dbProjects</arg>
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</spark>
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<ok to="create_updates"/>
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<error to="Kill"/>
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</action>
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<action name="create_updates">
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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>ProjectProgrammeAS</name>
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<class>eu.dnetlib.dhp.actionmanager.project.SparkAtomicActionJob</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${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}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=3840
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</spark-opts>
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<arg>--projectPath</arg><arg>${workingDir}/preparedProjects</arg>
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<arg>--programmePath</arg><arg>${workingDir}/preparedProgramme</arg>
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<arg>--topicPath</arg><arg>${workingDir}/topic</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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