changed the way to produce the AS for bipFinder.
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4eb8276493
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6fb6236cd4
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@ -1,86 +0,0 @@
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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.Objects;
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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.JavaSparkContext;
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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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/**
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* Just collects all the atomic actions produced for the different results and saves them in
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* outputpath for the ActionSet
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*/
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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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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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Objects
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.requireNonNull(
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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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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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@ -50,7 +50,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
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.toString(
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SparkAtomicActionScoreJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
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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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@ -69,14 +69,6 @@ public class SparkAtomicActionScoreJob implements Serializable {
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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final String bipScorePath = parser.get("bipScorePath");
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log.info("bipScorePath: {}", bipScorePath);
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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@ -84,12 +76,11 @@ public class SparkAtomicActionScoreJob implements Serializable {
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz);
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prepareResults(spark, inputPath, outputPath);
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});
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}
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private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath,
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String bipScorePath, Class<I> inputClazz) {
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private static <I extends Result> void prepareResults(SparkSession spark, String bipScorePath, String outputPath) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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@ -105,26 +96,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
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return bs;
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}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class));
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Dataset<I> results = readPath(spark, inputPath, inputClazz);
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results.createOrReplaceTempView("result");
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Dataset<Row> preparedResult = spark
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.sql(
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"select id " +
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"from result " +
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"where dataInfo.deletedbyinference = false ");
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bipScores
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.joinWith(
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preparedResult, bipScores.col("id").equalTo(preparedResult.col("id")),
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"inner")
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.map((MapFunction<Tuple2<BipScore, Row>, BipScore>) value -> {
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BipScore ret = value._1();
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ret.setId(value._1().getId());
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return ret;
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}, Encoders.bean(BipScore.class))
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.map((MapFunction<BipScore, Result>) bs -> {
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Result ret = new Result();
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@ -136,7 +108,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
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return ret;
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}, Encoders.bean(Result.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(inputClazz, p))
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.map(p -> new AtomicAction(Result.class, p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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@ -49,6 +49,25 @@
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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>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="deleteoutputpath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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@ -64,14 +83,8 @@
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<error to="Kill"/>
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</action>
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<fork name="atomicactions">
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<path start="atomicactions_publication"/>
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<path start="atomicactions_dataset"/>
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<path start="atomicactions_orp"/>
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<path start="atomicactions_software"/>
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</fork>
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<action name="atomicactions_publication">
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<action name="atomicactions">
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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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@ -88,118 +101,14 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${inputPath}/publication</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
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<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
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</spark>
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<ok to="join_aa"/>
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<error to="Kill"/>
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</action>
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<action name="atomicactions_dataset">
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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>Produces the atomic action with the bip finder scores for datasets</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${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>--inputPath</arg><arg>${inputPath}/dataset</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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<arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
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<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
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</spark>
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<ok to="join_aa"/>
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<error to="Kill"/>
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</action>
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<action name="atomicactions_orp">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Produces the atomic action with the bip finder scores for orp</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
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<jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
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<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
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</spark>
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<ok to="join_aa"/>
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<error to="Kill"/>
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</action>
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<action name="atomicactions_software">
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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>Produces the atomic action with the bip finder scores for software</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${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>--inputPath</arg><arg>${inputPath}/software</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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<arg>--outputPath</arg><arg>${workingDir}/software</arg>
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<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
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</spark>
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<ok to="join_aa"/>
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<error to="Kill"/>
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</action>
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<join name="join_aa" to="collectandsave"/>
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<action name="collectandsave">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>saves all the aa produced for the several types of results in the as output path</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave</class>
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<jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingDir}</arg>
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<arg>--inputPath</arg><arg>${bipScorePath}</arg>
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<arg>--outputPath</arg><arg>${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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