merge upstream

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java

@@ -15,7 +15,7 @@ public class EnrichMissingProject extends UpdateMatcher<OaBrokerProject> {
 		super(20,
 			prj -> Topic.ENRICH_MISSING_PROJECT,
 			(p, prj) -> p.getProjects().add(prj),
-			prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode());
+			prj -> prj.getOpenaireId());
 	}
 
 	@Override

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java

@@ -18,31 +18,25 @@ public class EnrichMoreProject extends UpdateMatcher<OaBrokerProject> {
 		super(20,
 			prj -> Topic.ENRICH_MORE_PROJECT,
 			(p, prj) -> p.getProjects().add(prj),
-			prj -> projectAsString(prj));
+			prj -> prj.getOpenaireId());
-	}
-
-	private static String projectAsString(final OaBrokerProject prj) {
-		return prj.getFunder() + "::" + prj.getFundingProgram() + "::" + prj.getCode();
 	}
 
 	@Override
 	protected List<OaBrokerProject> findDifferences(final OaBrokerMainEntity source,
 		final OaBrokerMainEntity target) {
 
-		if (target.getProjects().size() >= BrokerConstants.MAX_LIST_SIZE) {
+		if (target.getProjects().size() >= BrokerConstants.MAX_LIST_SIZE) { return new ArrayList<>(); }
-			return new ArrayList<>();
-		}
 
 		final Set<String> existingProjects = target
 			.getProjects()
 			.stream()
-			.map(EnrichMoreProject::projectAsString)
+			.map(p -> p.getOpenaireId())
 			.collect(Collectors.toSet());
 
 		return source
 			.getProjects()
 			.stream()
-			.filter(p -> !existingProjects.contains(projectAsString(p)))
+			.filter(p -> !existingProjects.contains(p.getOpenaireId()))
 			.collect(Collectors.toList());
 	}
 

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java

@@ -44,9 +44,7 @@ public class ConversionUtils {
 	private static final Logger log = LoggerFactory.getLogger(ConversionUtils.class);
 
 	public static List<OaBrokerInstance> oafInstanceToBrokerInstances(final Instance i) {
-		if (i == null) {
+		if (i == null) { return new ArrayList<>(); }
-			return new ArrayList<>();
-		}
 
 		return mappedList(i.getUrl(), url -> {
 			final OaBrokerInstance res = new OaBrokerInstance();
@@ -67,9 +65,7 @@ public class ConversionUtils {
 	}
 
 	public static final OaBrokerRelatedDataset oafDatasetToBrokerDataset(final Dataset d) {
-		if (d == null) {
+		if (d == null) { return null; }
-			return null;
-		}
 
 		final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset();
 		res.setOpenaireId(d.getId());
@@ -82,9 +78,7 @@ public class ConversionUtils {
 	}
 
 	public static OaBrokerRelatedPublication oafPublicationToBrokerPublication(final Publication p) {
-		if (p == null) {
+		if (p == null) { return null; }
-			return null;
-		}
 
 		final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication();
 		res.setOpenaireId(p.getId());
@@ -98,9 +92,7 @@ public class ConversionUtils {
 	}
 
 	public static final OaBrokerMainEntity oafResultToBrokerResult(final Result result) {
-		if (result == null) {
+		if (result == null) { return null; }
-			return null;
-		}
 
 		final OaBrokerMainEntity res = new OaBrokerMainEntity();
 
@@ -117,8 +109,7 @@ public class ConversionUtils {
 		res.setEmbargoenddate(fieldValue(result.getEmbargoenddate()));
 		res.setContributor(fieldList(result.getContributor()));
 		res
-			.setJournal(
+			.setJournal(result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null);
-				result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null);
 		res.setCollectedFromId(mappedFirst(result.getCollectedfrom(), KeyValue::getKey));
 		res.setCollectedFromName(mappedFirst(result.getCollectedfrom(), KeyValue::getValue));
 		res.setPids(mappedList(result.getPid(), ConversionUtils::oafPidToBrokerPid));
@@ -130,9 +121,7 @@ public class ConversionUtils {
 	}
 
 	private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) {
-		if (author == null) {
+		if (author == null) { return null; }
-			return null;
-		}
 
 		final String pids = author.getPid() != null ? author
 			.getPid()
@@ -142,6 +131,7 @@ public class ConversionUtils {
 			.filter(pid -> pid.getQualifier().getClassid() != null)
 			.filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid"))
 			.map(pid -> pid.getValue())
+			.map(pid -> cleanOrcid(pid))
 			.filter(StringUtils::isNotBlank)
 			.findFirst()
 			.orElse(null) : null;
@@ -149,10 +139,13 @@ public class ConversionUtils {
 		return new OaBrokerAuthor(author.getFullname(), pids);
 	}
 
+	private static String cleanOrcid(final String s) {
+		final String match = "//orcid.org/";
+		return s.contains(match) ? StringUtils.substringAfter(s, match) : s;
+	}
+
 	private static OaBrokerJournal oafJournalToBrokerJournal(final Journal journal) {
-		if (journal == null) {
+		if (journal == null) { return null; }
-			return null;
-		}
 
 		final OaBrokerJournal res = new OaBrokerJournal();
 		res.setName(journal.getName());
@@ -164,9 +157,7 @@ public class ConversionUtils {
 	}
 
 	private static OaBrokerExternalReference oafExtRefToBrokerExtRef(final ExternalReference ref) {
-		if (ref == null) {
+		if (ref == null) { return null; }
-			return null;
-		}
 
 		final OaBrokerExternalReference res = new OaBrokerExternalReference();
 		res.setRefidentifier(ref.getRefidentifier());
@@ -177,9 +168,7 @@ public class ConversionUtils {
 	}
 
 	public static final OaBrokerProject oafProjectToBrokerProject(final Project p) {
-		if (p == null) {
+		if (p == null) { return null; }
-			return null;
-		}
 
 		final OaBrokerProject res = new OaBrokerProject();
 		res.setOpenaireId(p.getId());
@@ -203,9 +192,7 @@ public class ConversionUtils {
 	}
 
 	public static final OaBrokerRelatedSoftware oafSoftwareToBrokerSoftware(final Software sw) {
-		if (sw == null) {
+		if (sw == null) { return null; }
-			return null;
-		}
 
 		final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware();
 		res.setOpenaireId(sw.getId());
@@ -268,9 +255,7 @@ public class ConversionUtils {
 	}
 
 	private static List<OaBrokerTypedValue> structPropTypedList(final List<StructuredProperty> list) {
-		if (list == null) {
+		if (list == null) { return new ArrayList<>(); }
-			return new ArrayList<>();
-		}
 
 		return list
 			.stream()
@@ -280,9 +265,7 @@ public class ConversionUtils {
 	}
 
 	private static <F, T> List<T> mappedList(final List<F> list, final Function<F, T> func) {
-		if (list == null) {
+		if (list == null) { return new ArrayList<>(); }
-			return new ArrayList<>();
-		}
 
 		return list
 			.stream()
@@ -293,9 +276,7 @@ public class ConversionUtils {
 	}
 
 	private static <F, T> List<T> flatMappedList(final List<F> list, final Function<F, List<T>> func) {
-		if (list == null) {
+		if (list == null) { return new ArrayList<>(); }
-			return new ArrayList<>();
-		}
 
 		return list
 			.stream()
@@ -307,9 +288,7 @@ public class ConversionUtils {
 	}
 
 	private static <F, T> T mappedFirst(final List<F> list, final Function<F, T> func) {
-		if (list == null) {
+		if (list == null) { return null; }
-			return null;
-		}
 
 		return list
 			.stream()

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Deduper.java

@@ -37,7 +37,7 @@ public class Deduper implements Serializable {
 	public static JavaPairRDD<String, Block> createSortedBlocks(
 		JavaPairRDD<String, MapDocument> mapDocs, DedupConfig config) {
 		final String of = config.getWf().getOrderField();
-		final int maxQueueSize = config.getWf().getGroupMaxSize();
+		final int maxQueueSize = config.getWf().getQueueMaxSize();
 
 		return mapDocs
 			// the reduce is just to be sure that we haven't document with same id

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/workflow.xml

@@ -0,0 +1,157 @@
+<workflow-app name="import Claims as Graph" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>reuseContent</name>
+            <value>false</value>
+            <description>should import content from the aggregator or reuse a previous version</description>
+        </property>
+        <property>
+            <name>contentPath</name>
+            <description>path location to store (or reuse) content from the aggregator</description>
+        </property>
+        <property>
+            <name>postgresURL</name>
+            <description>the postgres URL to access to the database</description>
+        </property>
+        <property>
+            <name>postgresUser</name>
+            <description>the user postgres</description>
+        </property>
+        <property>
+            <name>postgresPassword</name>
+            <description>the password postgres</description>
+        </property>
+        <property>
+            <name>dbSchema</name>
+            <value>beta</value>
+            <description>the database schema according to the D-Net infrastructure (beta or production)</description>
+        </property>
+        <property>
+            <name>mongoURL</name>
+            <description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
+        </property>
+        <property>
+            <name>mongoDb</name>
+            <description>mongo database</description>
+        </property>
+        <property>
+            <name>isLookupUrl</name>
+            <description>the address of the lookUp service</description>
+        </property>
+
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+        </configuration>
+    </global>
+
+	<start to="ImportDB_claims"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="ImportDB_claims">
+        <java>
+            <prepare>
+                <delete path="${contentPath}/db_claims"/>
+            </prepare>
+            <main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
+            <arg>--hdfsPath</arg><arg>${contentPath}/db_claims</arg>
+            <arg>--postgresUrl</arg><arg>${postgresURL}</arg>
+            <arg>--postgresUser</arg><arg>${postgresUser}</arg>
+            <arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--action</arg><arg>claims</arg>
+            <arg>--dbschema</arg><arg>${dbSchema}</arg>
+        </java>
+        <ok to="ImportODF_claims"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ImportODF_claims">
+        <java>
+            <prepare>
+                <delete path="${contentPath}/odf_claims"/>
+            </prepare>
+            <main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
+            <arg>-p</arg><arg>${contentPath}/odf_claims</arg>
+            <arg>-mongourl</arg><arg>${mongoURL}</arg>
+            <arg>-mongodb</arg><arg>${mongoDb}</arg>
+            <arg>-f</arg><arg>ODF</arg>
+            <arg>-l</arg><arg>store</arg>
+            <arg>-i</arg><arg>claim</arg>
+        </java>
+        <ok to="ImportOAF_claims"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ImportOAF_claims">
+        <java>
+            <prepare>
+                <delete path="${contentPath}/oaf_claims"/>
+            </prepare>
+            <main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
+            <arg>-p</arg><arg>${contentPath}/oaf_claims</arg>
+            <arg>-mongourl</arg><arg>${mongoURL}</arg>
+            <arg>-mongodb</arg><arg>${mongoDb}</arg>
+            <arg>-f</arg><arg>OAF</arg>
+            <arg>-l</arg><arg>store</arg>
+            <arg>-i</arg><arg>claim</arg>
+        </java>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/workflow.xml

@@ -1,169 +0,0 @@
-<workflow-app name="import Claims as Graph" xmlns="uri:oozie:workflow:0.5">
-    <parameters>
-        <property>
-            <name>migrationClaimsPathStep1</name>
-            <description>the base path to store hdfs file</description>
-        </property>
-        <property>
-            <name>migrationClaimsPathStep2</name>
-            <description>the temporary path to store entities before dispatching</description>
-        </property>
-        <property>
-            <name>migrationClaimsPathStep3</name>
-            <description>the graph Raw base path</description>
-        </property>
-        <property>
-            <name>postgresURL</name>
-            <description>the postgres URL to access to the database</description>
-        </property>
-        <property>
-            <name>postgresUser</name>
-            <description>the user postgres</description>
-        </property>
-        <property>
-            <name>postgresPassword</name>
-            <description>the password postgres</description>
-        </property>
-        <property>
-            <name>mongoURL</name>
-            <description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
-        </property>
-        <property>
-            <name>mongoDb</name>
-            <description>mongo database</description>
-        </property>
-        <property>
-            <name>sparkDriverMemory</name>
-            <description>memory for driver process</description>
-        </property>
-        <property>
-            <name>sparkExecutorMemory</name>
-            <description>memory for individual executor</description>
-        </property>
-        <property>
-            <name>sparkExecutorCores</name>
-            <description>number of cores used by single executor</description>
-        </property>
-    </parameters>
-
-	<start to="ResetWorkingPath"/>
-
-    <kill name="Kill">
-        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
-    </kill>
-
-    <action name="ResetWorkingPath">
-        <fs>
-            <delete path='${migrationClaimsPathStep1}'/>
-            <mkdir path='${migrationClaimsPathStep1}'/>
-        </fs>
-        <ok to="ImportDBClaims"/>
-        <error to="Kill"/>
-    </action>
-   
-    <action name="ImportDBClaims">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-            <main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
-            <arg>-p</arg><arg>${migrationClaimsPathStep1}/db_claims</arg>
-            <arg>-pgurl</arg><arg>${postgresURL}</arg>
-            <arg>-pguser</arg><arg>${postgresUser}</arg>
-            <arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
-            <arg>-a</arg><arg>claims</arg>
-        </java>
-		<ok to="ImportODFClaims"/>
-        <error to="Kill"/>
-    </action>
-    
-    <action name="ImportODFClaims">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-            <main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
-            <arg>-p</arg><arg>${migrationClaimsPathStep1}/odf_claims</arg>
-            <arg>-mongourl</arg><arg>${mongoURL}</arg>
-            <arg>-mongodb</arg><arg>${mongoDb}</arg>
-            <arg>-f</arg><arg>ODF</arg>
-            <arg>-l</arg><arg>store</arg>
-            <arg>-i</arg><arg>claim</arg>
-        </java>
-        <ok to="ImportOAFClaims"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="ImportOAFClaims">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-            <main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
-            <arg>-p</arg><arg>${migrationClaimsPathStep1}/oaf_claims</arg>
-            <arg>-mongourl</arg><arg>${mongoURL}</arg>
-            <arg>-mongodb</arg><arg>${mongoDb}</arg>
-            <arg>-f</arg><arg>OAF</arg>
-            <arg>-l</arg><arg>store</arg>
-            <arg>-i</arg><arg>claim</arg>
-        </java>
-        <ok to="ResetClaimEntities"/>
-        <error to="Kill"/>
-    </action>
-
-	<action name="ResetClaimEntities">
-        <fs>
-            <delete path='${migrationClaimsPathStep2}'/>
-            <mkdir path='${migrationClaimsPathStep2}'/>
-        </fs>
-        <ok to="GenerateClaimEntities"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="GenerateClaimEntities">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-            <master>yarn-cluster</master>
-            <mode>cluster</mode>
-            <name>GenerateClaimEntities</name>
-            <class>eu.dnetlib.dhp.migration.step2.GenerateEntitiesApplication</class>
-            <jar>dhp-aggregation-${projectVersion}.jar</jar>
-            <spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
-            <arg>-mt</arg> <arg>yarn-cluster</arg>
-            <arg>-s</arg><arg>${migrationClaimsPathStep1}/db_claims,${migrationClaimsPathStep1}/oaf_claims,${migrationClaimsPathStep1}/odf_claims</arg>
-            <arg>-t</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
-            <arg>-pgurl</arg><arg>${postgresURL}</arg>
-            <arg>-pguser</arg><arg>${postgresUser}</arg>
-            <arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
-        </spark>
-        <ok to="ResetClaimGraph"/>
-        <error to="Kill"/>
-    </action>
-
-	<action name="ResetClaimGraph">
-        <fs>
-            <delete path='${migrationClaimsPathStep3}'/>
-            <mkdir path='${migrationClaimsPathStep3}'/>
-        </fs>
-        <ok to="GenerateClaimGraph"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="GenerateClaimGraph">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-            <master>yarn-cluster</master>
-            <mode>cluster</mode>
-            <name>GenerateClaimGraph</name>
-            <class>eu.dnetlib.dhp.migration.step3.DispatchEntitiesApplication</class>
-            <jar>dhp-aggregation-${projectVersion}.jar</jar>
-            <spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
-            <arg>-mt</arg> <arg>yarn-cluster</arg>
-            <arg>-s</arg><arg>${migrationClaimsPathStep2}/claim_entities</arg>
-            <arg>-g</arg><arg>${migrationClaimsPathStep3}</arg>
-        </spark>
-        <ok to="End"/>
-        <error to="Kill"/>
-    </action>  
-
-    <end name="End"/>
-</workflow-app>

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJobTest.java

@@ -1,9 +1,10 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.io.IOException;
-import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
+import java.nio.file.Files;
-import eu.dnetlib.dhp.schema.oaf.Relation;
+import java.nio.file.Path;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.FilterFunction;
@@ -19,9 +20,10 @@ import org.junit.jupiter.api.io.TempDir;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.IOException;
+import com.fasterxml.jackson.databind.ObjectMapper;
-import java.nio.file.Files;
+
-import java.nio.file.Path;
+import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 
 public class PrepareRelationsJobTest {
 
@@ -74,14 +76,19 @@ public class PrepareRelationsJobTest {
 					"-maxRelations", String.valueOf(maxRelations)
 				});
 
-		Dataset<Relation> out = spark.read()
+		Dataset<Relation> out = spark
-				.parquet(testPath.toString())
+			.read()
-				.as(Encoders.bean(Relation.class))
+			.parquet(testPath.toString())
-				.cache();
+			.as(Encoders.bean(Relation.class))
+			.cache();
 
 		Assertions.assertEquals(10, out.count());
 
-		Dataset<Row> freq = out.toDF().cube(SUBRELTYPE).count().filter((FilterFunction<Row>) value -> !value.isNullAt(0));
+		Dataset<Row> freq = out
+			.toDF()
+			.cube(SUBRELTYPE)
+			.count()
+			.filter((FilterFunction<Row>) value -> !value.isNullAt(0));
 		long outcome = freq.filter(freq.col(SUBRELTYPE).equalTo(OUTCOME)).collectAsList().get(0).getAs("count");
 		long supplement = freq.filter(freq.col(SUBRELTYPE).equalTo(SUPPLEMENT)).collectAsList().get(0).getAs("count");