merge done

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

@@ -1,8 +1,8 @@
+
 package eu.dnetlib.dhp.oa.dedup;
 
 import java.io.IOException;
 
-import eu.dnetlib.dhp.oa.dedup.model.BlockStats;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaPairRDD;
@@ -15,8 +15,10 @@ import org.apache.spark.sql.SparkSession;
 import org.dom4j.DocumentException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.oa.dedup.model.Block;
+import eu.dnetlib.dhp.oa.dedup.model.BlockStats;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -56,6 +58,15 @@ public class SparkBlockStats extends AbstractSparkAction {
                 .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
     }
 
+    public Long computeComparisons(Long blockSize, Long slidingWindowSize){
+
+        if (slidingWindowSize >= blockSize)
+            return (slidingWindowSize * (slidingWindowSize - 1)) / 2;
+        else {
+            return (blockSize - slidingWindowSize + 1) * (slidingWindowSize * (slidingWindowSize - 1)) / 2;
+        }
+    }
+
 	@Override
 	public void run(ISLookUpService isLookUpService)
 		throws DocumentException, IOException, ISLookUpException {
@@ -93,13 +104,13 @@ public class SparkBlockStats extends AbstractSparkAction {
 			// create blocks for deduplication
 			JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf);
 
-            JavaRDD<BlockStats> blockStats = blocks.map(b ->
+			JavaRDD<BlockStats> blockStats = blocks
-                    new BlockStats(
+				.map(
+					b -> new BlockStats(
 						b._1(),
 						(long) b._2().getDocuments().size(),
 						computeComparisons(
-                                    (long) b._2().getDocuments().size(), (long) dedupConf.getWf().getSlidingWindowSize()))
+							(long) b._2().getDocuments().size(), (long) dedupConf.getWf().getSlidingWindowSize())));
-            );
 
 			// save the blockstats in the workingdir
 			spark
@@ -110,12 +121,4 @@ public class SparkBlockStats extends AbstractSparkAction {
 		}
 	}
 
-    public Long computeComparisons(Long blockSize, Long slidingWindowSize){
-
-        if (slidingWindowSize >= blockSize)
-            return (slidingWindowSize * (slidingWindowSize - 1)) / 2;
-        else {
-            return (blockSize - slidingWindowSize + 1) * (slidingWindowSize * (slidingWindowSize - 1)) / 2;
-        }
-    }
 }

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

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.oa.dedup.model;
 
 import java.io.Serializable;

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/statistics/oozie_app/workflow.xml

@@ -1,4 +1,4 @@
-<workflow-app name="Duplicate Scan" xmlns="uri:oozie:workflow:0.5">
+<workflow-app name="Create dedup blocks" xmlns="uri:oozie:workflow:0.5">
     <parameters>
         <property>
             <name>graphBasePath</name>
@@ -12,14 +12,6 @@
             <name>actionSetId</name>
             <description>id of the actionSet</description>
         </property>
-        <property>
-            <name>workingPath</name>
-            <description>path for the working directory</description>
-        </property>
-        <property>
-            <name>dedupGraphPath</name>
-            <description>path for the output graph</description>
-        </property>
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>
@@ -85,7 +77,7 @@
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>Create Similarity Relations</name>
+            <name>Create deduplication blocks</name>
             <class>eu.dnetlib.dhp.oa.dedup.SparkBlockStats</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
@@ -101,7 +93,7 @@
             <arg>--i</arg><arg>${graphBasePath}</arg>
             <arg>--la</arg><arg>${isLookUpUrl}</arg>
             <arg>--asi</arg><arg>${actionSetId}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--w</arg><arg>${workingDir}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java

@@ -1,8 +1,17 @@
+
 package eu.dnetlib.dhp.oa.dedup;
 
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import static java.nio.file.Files.createTempDirectory;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.Mockito.lenient;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.Serializable;
+import java.net.URISyntaxException;
+import java.nio.file.Paths;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
@@ -14,15 +23,9 @@ import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.junit.jupiter.MockitoExtension;
 
-import java.io.File;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import java.io.IOException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
-import java.io.Serializable;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import java.net.URISyntaxException;
-import java.nio.file.Paths;
-
-import static java.nio.file.Files.createTempDirectory;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.mockito.Mockito.lenient;
 
 @ExtendWith(MockitoExtension.class)
 public class SparkStatsTest implements Serializable {
@@ -172,4 +175,3 @@ public class SparkStatsTest implements Serializable {
 		assertEquals(55, orp_blocks);
 	}
 }
-