added output directory removal in the blacklist spark actions; included common global properties in blacklist's workflow.xml

dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/PrepareMergedRelationJob.java

@@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
 
 import java.util.Optional;
 
+import eu.dnetlib.dhp.common.HdfsSupport;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
@@ -56,6 +57,7 @@ public class PrepareMergedRelationJob {
 			conf,
 			isSparkSessionManaged,
 			spark -> {
+				removeOutputDir(spark, outputPath);
 				selectMergesRelations(
 					spark,
 					inputPath,
@@ -84,4 +86,9 @@ public class PrepareMergedRelationJob {
 				(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
 				Encoders.bean(Relation.class));
 	}
+
+	private static void removeOutputDir(SparkSession spark, String path) {
+		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+	}
+
 }

dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java

@@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 import java.util.Objects;
 import java.util.Optional;
 
+import eu.dnetlib.dhp.common.HdfsSupport;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
@@ -62,6 +63,7 @@ public class SparkRemoveBlacklistedRelationJob {
 			conf,
 			isSparkSessionManaged,
 			spark -> {
+				removeOutputDir(spark, outputPath);
 				removeBlacklistedRelations(
 					spark,
 					blacklistPath,
@@ -69,7 +71,6 @@ public class SparkRemoveBlacklistedRelationJob {
 					outputPath,
 					mergesPath);
 			});
-
 	}
 
 	private static void removeBlacklistedRelations(SparkSession spark, String blacklistPath, String inputPath,
@@ -144,4 +145,8 @@ public class SparkRemoveBlacklistedRelationJob {
 				Encoders.bean(Relation.class));
 	}
 
+	private static void removeOutputDir(SparkSession spark, String path) {
+		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+	}
+
 }

dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml

@@ -22,6 +22,25 @@
         </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="reset_outputpath"/>
 
     <kill name="Kill">
@@ -49,8 +68,6 @@
 
     <action name="copy_publication">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/publication</arg>
             <arg>${nameNode}/${outputPath}/publication</arg>
         </distcp>
@@ -60,8 +77,6 @@
 
     <action name="copy_dataset">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/dataset</arg>
             <arg>${nameNode}/${outputPath}/dataset</arg>
         </distcp>
@@ -71,8 +86,6 @@
 
     <action name="copy_orp">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/otherresearchproduct</arg>
             <arg>${nameNode}/${outputPath}/otherresearchproduct</arg>
         </distcp>
@@ -82,8 +95,6 @@
 
     <action name="copy_software">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/software</arg>
             <arg>${nameNode}/${outputPath}/software</arg>
         </distcp>
@@ -93,8 +104,6 @@
     
     <action name="copy_organization">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/organization</arg>
             <arg>${nameNode}/${outputPath}/organization</arg>
         </distcp>
@@ -104,8 +113,6 @@
 
     <action name="copy_project">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/project</arg>
             <arg>${nameNode}/${outputPath}/project</arg>
         </distcp>
@@ -115,8 +122,6 @@
 
     <action name="copy_datasource">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/datasource</arg>
             <arg>${nameNode}/${outputPath}/datasource</arg>
         </distcp>
@@ -128,8 +133,6 @@
 
     <action name="read_blacklist">
         <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <main-class>eu.dnetlib.dhp.blacklist.ReadBlacklistFromDB</main-class>
             <arg>--hdfsPath</arg><arg>${workingDir}/blacklist</arg>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
@@ -156,6 +159,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
             <arg>--outputPath</arg><arg>${workingDir}/mergesRelation</arg>
@@ -180,6 +184,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
             <arg>--outputPath</arg><arg>${outputPath}/relation</arg>