configurable number of partitions used in the SparkCreateSimRels phase

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

@@ -2,6 +2,7 @@
 package eu.dnetlib.dhp.oa.dedup;
 
 import java.io.IOException;
+import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
@@ -34,7 +35,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 
 	private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
 
-	public static final int NUM_PARTITIONS = 10000;
+	public static final int NUM_PARTITIONS = 1000;
 
 	public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) {
 		super(parser, spark);
@@ -63,7 +64,12 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 		final String isLookUpUrl = parser.get("isLookUpUrl");
 		final String actionSetId = parser.get("actionSetId");
 		final String workingPath = parser.get("workingPath");
+		final int numPartitions = Optional
+				.ofNullable(parser.get("numPartitions"))
+				.map(Integer::valueOf)
+				.orElse(NUM_PARTITIONS);
 
+		log.info("numPartitions: '{}'", numPartitions);
 		log.info("graphBasePath: '{}'", graphBasePath);
 		log.info("isLookUpUrl:   '{}'", isLookUpUrl);
 		log.info("actionSetId:   '{}'", actionSetId);
@@ -83,7 +89,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 
 			JavaPairRDD<String, MapDocument> mapDocuments = sc
 				.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
-				.repartition(NUM_PARTITIONS)
+				.repartition(numPartitions)
 				.mapToPair(
 					(PairFunction<String, String, MapDocument>) s -> {
 						MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
@@ -93,13 +99,13 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 			// create blocks for deduplication
 			JavaPairRDD<String, Block> blocks = Deduper
 				.createSortedBlocks(mapDocuments, dedupConf)
-				.repartition(NUM_PARTITIONS);
+				.repartition(numPartitions);
 
 			// create relations by comparing only elements in the same group
 			Deduper
 				.computeRelations(sc, blocks, dedupConf)
 				.map(t -> createSimRel(t._1(), t._2(), entity))
-				.repartition(NUM_PARTITIONS)
+				.repartition(numPartitions)
 				.map(r -> OBJECT_MAPPER.writeValueAsString(r))
 				.saveAsTextFile(outputPath);
 		}

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json

@@ -22,5 +22,11 @@
     "paramLongName": "workingPath",
     "paramDescription": "path of the working directory",
     "paramRequired": true
+  },
+  {
+    "paramName": "np",
+    "paramLongName": "numPartitions",
+    "paramDescription": "number of partitions for the similarity relations intermediate phases",
+    "paramRequired": false
   }
 ]

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

@@ -20,6 +20,10 @@
             <name>dedupGraphPath</name>
             <description>path for the output graph</description>
         </property>
+        <property>
+            <name>cutConnectedComponent</name>
+            <description>max number of elements in a connected component</description>
+        </property>
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>
@@ -106,10 +110,11 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--la</arg><arg>${isLookUpUrl}</arg>
+            <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
-            <arg>--asi</arg><arg>${actionSetId}</arg>
+            <arg>--actionSetId</arg><arg>${actionSetId}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--numPartitions</arg><arg>8000</arg>
         </spark>
         <ok to="CreateMergeRel"/>
         <error to="Kill"/>
@@ -132,10 +137,11 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
-            <arg>--la</arg><arg>${isLookUpUrl}</arg>
+            <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
-            <arg>--asi</arg><arg>${actionSetId}</arg>
+            <arg>--actionSetId</arg><arg>${actionSetId}</arg>
+            <arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
         </spark>
         <ok to="CreateDedupRecord"/>
         <error to="Kill"/>
@@ -158,10 +164,10 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
-            <arg>--la</arg><arg>${isLookUpUrl}</arg>
+            <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
-            <arg>--asi</arg><arg>${actionSetId}</arg>
+            <arg>--actionSetId</arg><arg>${actionSetId}</arg>
         </spark>
         <ok to="UpdateEntity"/>
         <error to="Kill"/>
@@ -184,9 +190,9 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
-            <arg>--o</arg><arg>${dedupGraphPath}</arg>
+            <arg>--dedupGraphPath</arg><arg>${dedupGraphPath}</arg>
         </spark>
         <ok to="copyRelations"/>
         <error to="Kill"/>

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json

@@ -1,17 +1,17 @@
 [
-{
+  {
-  "paramName": "i",
+    "paramName": "i",
-  "paramLongName": "graphBasePath",
+    "paramLongName": "graphBasePath",
-  "paramDescription": "the base path of raw graph",
+    "paramDescription": "the base path of raw graph",
-  "paramRequired": true
+    "paramRequired": true
-},
+  },
-{
+  {
-  "paramName": "w",
+    "paramName": "w",
-  "paramLongName": "workingPath",
+    "paramLongName": "workingPath",
-  "paramDescription": "the working directory path",
+    "paramDescription": "the working directory path",
-  "paramRequired": true
+    "paramRequired": true
-},
+  },
-{
+  {
     "paramName": "o",
     "paramLongName": "dedupGraphPath",
     "paramDescription": "the path of the dedup graph",