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Changes to actionsets 

Resolve comments from
#355
This commit is contained in:
dimitrispie 2023-11-14 09:46:52 +02:00
parent 89c4dfbaf4
commit d524e30866
9 changed files with 116 additions and 469 deletions
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39
dhp-workflows/dhp-stats-actionsets/pom.xml
View File

@ -8,46 +8,7 @@
</parent>
<artifactId>dhp-stats-actionsets</artifactId>
<!-- <build>-->
<!-- <plugins>-->
<!-- <plugin>-->
<!-- <groupId>net.alchim31.maven</groupId>-->
<!-- <artifactId>scala-maven-plugin</artifactId>-->
<!-- <version>${net.alchim31.maven.version}</version>-->
<!-- <executions>-->
<!-- <execution>-->
<!-- <id>scala-compile-first</id>-->
<!-- <phase>initialize</phase>-->
<!-- <goals>-->
<!-- <goal>add-source</goal>-->
<!-- <goal>compile</goal>-->
<!-- </goals>-->
<!-- </execution>-->
<!-- <execution>-->
<!-- <id>scala-test-compile</id>-->
<!-- <phase>process-test-resources</phase>-->
<!-- <goals>-->
<!-- <goal>testCompile</goal>-->
<!-- </goals>-->
<!-- </execution>-->
<!-- <execution>-->
<!-- <id>scala-doc</id>-->
<!-- <phase>process-resources</phase> &lt;!&ndash; or wherever &ndash;&gt;-->
<!-- <goals>-->
<!-- <goal>doc</goal>-->
<!-- </goals>-->
<!-- </execution>-->
<!-- </executions>-->
<!-- <configuration>-->
<!-- <scalaVersion>${scala.version}</scalaVersion>-->
<!-- </configuration>-->
<!-- </plugin>-->
<!-- </plugins>-->
<!-- </build>-->
<dependencies>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>

102
dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
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@ -1,102 +0,0 @@
package eu.dnetlib.dhp.actionmanager;
import java.util.Optional;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.Subject;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
public class Constants {
public static final String DOI = "doi";
public static final String DOI_CLASSNAME = "Digital Object Identifier";
public static final String DEFAULT_DELIMITER = ",";
public static final String DEFAULT_FOS_DELIMITER = "\t";
public static final String UPDATE_DATA_INFO_TYPE = "update";
// public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos";
public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE";
// public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip";
// public static final String UPDATE_SUBJECT_SDG_CLASS_ID = "subject:sdg";
// public static final String UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID = "measure:usage_counts";
// public static final String UPDATE_KEY_USAGE_COUNTS = "count";
public static final String UPDATE_MEASURE_STATS_MODEL_CLASS_ID = "measure:stats_model";
public static final String UPDATE_KEY_STATS_MODEL = "stats_model";
// public static final String UPDATE_MEASURE_PUBLICLY_FUNDED_CLASS_ID = "measure:publicly_funded";
// public static final String UPDATE_KEY_PUBLICLY_FUNDED = "publicly_funded";
// public static final String FOS_CLASS_ID = "FOS";
// public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification";
//
// public static final String SDG_CLASS_ID = "SDG";
// public static final String SDG_CLASS_NAME = "Sustainable Development Goals";
public static final String NULL = "NULL";
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private Constants() {
}
public static Boolean isSparkSessionManaged(ArgumentApplicationParser parser) {
return Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
public static Subject getSubject(String sbj, String classid, String classname,
String diqualifierclassid) {
if (sbj == null || sbj.equals(NULL))
return null;
Subject s = new Subject();
s.setValue(sbj);
s
.setQualifier(
OafMapperUtils
.qualifier(
classid,
classname,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
ModelConstants.DNET_SUBJECT_TYPOLOGIES));
s
.setDataInfo(
OafMapperUtils
.dataInfo(
false,
UPDATE_DATA_INFO_TYPE,
true,
false,
OafMapperUtils
.qualifier(
diqualifierclassid,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
""));
return s;
}
}

206
dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsAtomicActionsJob.java
View File

@ -1,7 +1,6 @@
package eu.dnetlib.dhp.actionmanager.stats_actionsets;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.io.Serializable;
@ -12,14 +11,22 @@ import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.types.DataTypes;
import org.apache.spark.sql.types.StructField;
import org.apache.spark.sql.types.StructType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -65,6 +72,9 @@ public class StatsAtomicActionsJob implements Serializable {
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
conf.set("spark.speculation", "false");
conf.set("spark.hadoop.mapreduce.map.speculative", "false");
conf.set("spark.hadoop.mapreduce.reduce.speculative", "false");
final String dbname = parser.get("statsDB");
@ -75,75 +85,26 @@ public class StatsAtomicActionsJob implements Serializable {
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
prepareGreenData(dbname, spark, workingPath + "/greenOADB", "indi_pub_green_oa", "id");
prepareDiamondData(dbname, spark, workingPath + "/diamondOADΒ", "indi_pub_diamond", "id");
preparePubliclyFundedData(
dbname, spark, workingPath + "/publiclyFundedDΒ", "indi_funded_result_with_fundref", "id");
prepareOAColourData(dbname, spark, workingPath + "/oacolourDB", "", "id");
prepareResultEnhancement(dbname, spark, workingPath + "/resultEnhancements", "id");
writeActionSet(spark, workingPath, outputPath);
});
}
private static void prepareGreenData(String dbname, SparkSession spark, String workingPath, String tableName,
private static void prepareResultEnhancement(String dbname, SparkSession spark, String workingPath,
String resultAttributeName) {
spark
.sql(
String
.format(
"select %s as id, green_oa as green_oa " +
"from %s.%s",
resultAttributeName, dbname, tableName))
.as(Encoders.bean(StatsGreenOAModel.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath);
}
private static void prepareDiamondData(String dbname, SparkSession spark, String workingPath, String tableName,
String resultAttributeName) {
spark
.sql(
String
.format(
"select %s as id, in_diamond_journal as in_diamond_journal " +
"from %s.%s",
resultAttributeName, dbname, tableName))
.as(Encoders.bean(StatsDiamondOAModel.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath);
}
private static void preparePubliclyFundedData(String dbname, SparkSession spark, String workingPath,
String tableName,
String resultAttributeName) {
spark
.sql(
String
.format(
"select %s as id, fundref as publicly_funded " +
"from %s.%s",
resultAttributeName, dbname, tableName))
.as(Encoders.bean(StatsPubliclyFundedModel.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath);
}
private static void prepareOAColourData(String dbname, SparkSession spark, String workingPath, String tableName,
String resultAttributeName) {
spark
.sql(
String
.format(
"select b.%s as id, is_gold, is_bronze_oa, is_hybrid from %s.indi_pub_bronze_oa b " +
"select b.%s as id, is_gold, is_bronze_oa, is_hybrid,green_oa, in_diamond_journal,f.fundref as publicly_funded "
+ "from %s.indi_pub_bronze_oa b " +
"left outer join %s.indi_pub_gold_oa g on g.id=b.id " +
"left outer join %s.indi_pub_hybrid h on b.id=h.id",
resultAttributeName, dbname, dbname, dbname))
.as(Encoders.bean(StatsOAColourModel.class))
"left outer join %s.indi_pub_hybrid h on b.id=h.id " +
"left outer join %s.indi_pub_green_oa gr on b.id=gr.id " +
"left outer join %s.indi_pub_diamond d on b.id=d.id " +
"left outer join %s.indi_funded_result_with_fundref f on b.id=f.id ",
resultAttributeName, dbname, dbname, dbname, dbname, dbname, dbname))
.as(Encoders.bean(StatsResultEnhancementModel.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
@ -152,125 +113,39 @@ public class StatsAtomicActionsJob implements Serializable {
public static void writeActionSet(SparkSession spark, String inputPath, String outputPath) {
getFinalIndicatorsGreenResult(spark, inputPath + "/greenOADB")
getResultEnhancements(spark, inputPath + "/resultEnhancements")
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p))
.union(
getFinalIndicatorsDiamondResult(spark, inputPath + "/diamondOADΒ")
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p)))
.union(
getFinalIndicatorsPubliclyFundedResult(spark, inputPath + "/publiclyFundedDΒ")
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p)))
.union(
getFinalIndicatorsOAColourResult(spark, inputPath + "/oacolourDB")
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p)))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
.saveAsHadoopFile(
outputPath,
Text.class,
Text.class,
SequenceFileOutputFormat.class,
GzipCodec.class);
}
public static Measure newMeasureInstance(String id) {
Measure m = new Measure();
m.setId(id);
m.setUnit(new ArrayList<>());
return m;
}
private static Dataset<Result> getResultEnhancements(SparkSession spark, String inputPath) {
private static Dataset<Result> getFinalIndicatorsGreenResult(SparkSession spark, String inputPath) {
return readPath(spark, inputPath, StatsGreenOAModel.class)
.map((MapFunction<StatsGreenOAModel, Result>) usm -> {
return readPath(spark, inputPath, StatsResultEnhancementModel.class)
.map((MapFunction<StatsResultEnhancementModel, Result>) usm -> {
Result r = new Result();
r.setId("50|" + usm.getId());
r.setMeasures(getMeasure(usm.isGreen_oa(), "green_oa"));
r.setIsInDiamondJournal(usm.isIn_diamond_journal());
r.setIsGreen(usm.isGreen_oa());
r.setPubliclyFunded(usm.isPublicly_funded());
if (usm.isIs_bronze_oa())
r.setOpenAccessColor(OpenAccessColor.bronze);
else if (usm.isIs_gold())
r.setOpenAccessColor(OpenAccessColor.bronze);
else if (usm.isIs_gold())
r.setOpenAccessColor(OpenAccessColor.gold);
return r;
}, Encoders.bean(Result.class));
}
private static Dataset<Result> getFinalIndicatorsDiamondResult(SparkSession spark, String inputPath) {
return readPath(spark, inputPath, StatsDiamondOAModel.class)
.map((MapFunction<StatsDiamondOAModel, Result>) usm -> {
Result r = new Result();
r.setId("50|" + usm.getId());
r.setMeasures(getMeasure(usm.isIn_diamond_journal(), "in_diamond_journal"));
return r;
}, Encoders.bean(Result.class));
}
private static Dataset<Result> getFinalIndicatorsPubliclyFundedResult(SparkSession spark, String inputPath) {
return readPath(spark, inputPath, StatsPubliclyFundedModel.class)
.map((MapFunction<StatsPubliclyFundedModel, Result>) usm -> {
Result r = new Result();
r.setId("50|" + usm.getId());
r.setMeasures(getMeasure(usm.isPublicly_funded(), "publicly_funded"));
return r;
}, Encoders.bean(Result.class));
}
private static Dataset<Result> getFinalIndicatorsOAColourResult(SparkSession spark, String inputPath) {
return readPath(spark, inputPath, StatsOAColourModel.class)
.map((MapFunction<StatsOAColourModel, Result>) usm -> {
Result r = new Result();
r.setId("50|" + usm.getId());
r.setMeasures(getMeasureOAColour(usm.isIs_gold(), usm.isIs_bronze_oa(), usm.isIs_hybrid()));
return r;
}, Encoders.bean(Result.class));
}
private static List<Measure> getMeasure(Boolean is_model_oa, String model_type) {
DataInfo dataInfo = OafMapperUtils
.dataInfo(
false,
UPDATE_DATA_INFO_TYPE,
true,
false,
OafMapperUtils
.qualifier(
UPDATE_MEASURE_STATS_MODEL_CLASS_ID,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
"");
return Arrays
.asList(
OafMapperUtils
.newMeasureInstance(model_type, String.valueOf(is_model_oa), UPDATE_KEY_STATS_MODEL, dataInfo));
}
private static List<Measure> getMeasureOAColour(Boolean is_gold, Boolean is_bronze_oa, Boolean is_hybrid) {
DataInfo dataInfo = OafMapperUtils
.dataInfo(
false,
UPDATE_DATA_INFO_TYPE,
true,
false,
OafMapperUtils
.qualifier(
UPDATE_MEASURE_STATS_MODEL_CLASS_ID,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
"");
return Arrays
.asList(
OafMapperUtils
.newMeasureInstance("is_gold", String.valueOf(is_gold), UPDATE_KEY_STATS_MODEL, dataInfo),
OafMapperUtils
.newMeasureInstance("is_bronze_oa", String.valueOf(is_bronze_oa), UPDATE_KEY_STATS_MODEL, dataInfo),
OafMapperUtils
.newMeasureInstance("is_hybrid", String.valueOf(is_hybrid), UPDATE_KEY_STATS_MODEL, dataInfo));
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
@ -282,5 +157,4 @@ public class StatsAtomicActionsJob implements Serializable {
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
}

29
dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsDiamondOAModel.java
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@ -1,29 +0,0 @@
package eu.dnetlib.dhp.actionmanager.stats_actionsets;
import java.io.Serializable;
/**
* @author dimitris.pierrakos
* @Date 30/10/23
*/
public class StatsDiamondOAModel implements Serializable {
private String id;
private boolean in_diamond_journal;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public boolean isIn_diamond_journal() {
return in_diamond_journal;
}
public void setIn_diamond_journal(boolean in_diamond_journal) {
this.in_diamond_journal = in_diamond_journal;
}
}

29
dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsGreenOAModel.java
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@ -1,29 +0,0 @@
package eu.dnetlib.dhp.actionmanager.stats_actionsets;
import java.io.Serializable;
/**
* @author dimitris.pierrakos
* @Date 30/10/23
*/
public class StatsGreenOAModel implements Serializable {
private String id;
private boolean green_oa;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public boolean isGreen_oa() {
return green_oa;
}
public void setGreen_oa(boolean green_oa) {
this.green_oa = green_oa;
}
}

47
dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsOAColourModel.java
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@ -1,47 +0,0 @@
package eu.dnetlib.dhp.actionmanager.stats_actionsets;
import java.io.Serializable;
/**
* @author dimitris.pierrakos
* @Date 30/10/23
*/
public class StatsOAColourModel implements Serializable {
private String id;
private boolean is_gold;
private boolean is_bronze_oa;
private boolean is_hybrid;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public boolean isIs_gold() {
return is_gold;
}
public void setIs_gold(boolean is_gold) {
this.is_gold = is_gold;
}
public boolean isIs_bronze_oa() {
return is_bronze_oa;
}
public void setIs_bronze_oa(boolean is_bronze_oa) {
this.is_bronze_oa = is_bronze_oa;
}
public boolean isIs_hybrid() {
return is_hybrid;
}
public void setIs_hybrid(boolean is_hybrid) {
this.is_hybrid = is_hybrid;
}
}

29
dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsPubliclyFundedModel.java
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@ -1,29 +0,0 @@
package eu.dnetlib.dhp.actionmanager.stats_actionsets;
import java.io.Serializable;
/**
* @author dimitris.pierrakos
* @Date 30/10/23
*/
public class StatsPubliclyFundedModel implements Serializable {
private String id;
private boolean publicly_funded;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public boolean isPublicly_funded() {
return publicly_funded;
}
public void setPublicly_funded(boolean publicly_funded) {
this.publicly_funded = publicly_funded;
}
}

76
dhp-workflows/dhp-stats-actionsets/src/main/java/eu/dnetlib/dhp/actionmanager/stats_actionsets/StatsResultEnhancementModel.java Normal file
View File

@ -0,0 +1,76 @@
package eu.dnetlib.dhp.actionmanager.stats_actionsets;
import java.io.Serializable;
import eu.dnetlib.dhp.schema.oaf.*;
/**
* @author dimitris.pierrakos
* @Date 30/10/23
*/
public class StatsResultEnhancementModel implements Serializable {
private String id;
private Boolean is_gold;
private Boolean is_bronze_oa;
private Boolean is_hybrid;
private boolean in_diamond_journal;
private boolean green_oa;
private boolean publicly_funded;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public Boolean isIs_gold() {
return is_gold;
}
public void setIs_gold(Boolean is_gold) {
this.is_gold = is_gold;
}
public Boolean isIs_bronze_oa() {
return is_bronze_oa;
}
public void setIs_bronze_oa(Boolean is_bronze_oa) {
this.is_bronze_oa = is_bronze_oa;
}
public Boolean isIs_hybrid() {
return is_hybrid;
}
public void setIs_hybrid(Boolean is_hybrid) {
this.is_hybrid = is_hybrid;
}
public boolean isIn_diamond_journal() {
return in_diamond_journal;
}
public void setIn_diamond_journal(boolean in_diamond_journal) {
this.in_diamond_journal = in_diamond_journal;
}
public boolean isGreen_oa() {
return green_oa;
}
public void setGreen_oa(boolean green_oa) {
this.green_oa = green_oa;
}
public boolean isPublicly_funded() {
return publicly_funded;
}
public void setPublicly_funded(boolean publicly_funded) {
this.publicly_funded = publicly_funded;
}
}

28
dhp-workflows/dhp-stats-actionsets/src/main/resources/eu/dnetlib/dhp/actionmanager/stats_actionsets/oozie_app/workflow.xml
View File

@ -68,39 +68,11 @@
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="atomicactions">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the usage stats count for results</name>
<!-- <class>eu.dnetlib.dhp.actionmanager.stats_actionsets.SparkAtomicActionUsageJob</class>-->
<class>eu.dnetlib.dhp.actionmanager.stats_actionsets.SparkAtomicActionGreenOAJob</class>
<jar>dhp-stats-actionsets-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--hive_metastore_uris</arg><arg>${hiveMetastoreUris}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--statsDB</arg><arg>${statsDB}</arg>
<arg>--workingPath</arg><arg>${workingDir}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="atomicactionsStats">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the stats green_oa for results</name>
<!-- <class>eu.dnetlib.dhp.actionmanager.stats_actionsets.SparkAtomicActionUsageJob</class>-->
<class>eu.dnetlib.dhp.actionmanager.stats_actionsets.StatsAtomicActionsJob</class>
<jar>dhp-stats-actionsets-${projectVersion}.jar</jar>
<spark-opts>