roots wf merged in scan wf

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

@@ -42,14 +42,14 @@ public class SparkCreateSimRels implements Serializable {
 
         //read oozie parameters
         final String graphBasePath = parser.get("graphBasePath");
-        final String rawSet = parser.get("rawSet");
         final String isLookUpUrl = parser.get("isLookUpUrl");
+        final String rawSet = parser.get("rawSet");
         final String actionSetId = parser.get("actionSetId");
         final String workingPath = parser.get("workingPath");
 
         System.out.println(String.format("graphBasePath: '%s'", graphBasePath));
-        System.out.println(String.format("rawSet: '%s'", rawSet));
         System.out.println(String.format("isLookUpUrl: '%s'", isLookUpUrl));
+        System.out.println(String.format("rawSet: '%s'", rawSet));
         System.out.println(String.format("actionSetId: '%s'", actionSetId));
         System.out.println(String.format("workingPath: '%s'", workingPath));
 
@@ -84,13 +84,16 @@ public class SparkCreateSimRels implements Serializable {
                         .mode("overwrite")
                         .save(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity));
 
+                if (rawSet != null) {
                     //create atomic actions
                     JavaRDD<Tuple2<Text, Text>> newSimRels = relationsRDD
                             .map(this::createSequenceFileRow);
 
                     simRel = simRel.union(newSimRels);
                 }
+            }
 
+            if (rawSet != null)
                 simRel.mapToPair(r -> r)
                     .saveAsHadoopFile(rawSet, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
         }

dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dhp/dedup/SparkUpdateEntity.java

@@ -21,8 +21,9 @@ import org.apache.spark.sql.SparkSession;
 import scala.Tuple2;
 
 import java.io.IOException;
+import java.io.Serializable;
 
-public class SparkUpdateEntity {
+public class SparkUpdateEntity implements Serializable {
 
     final String IDJSONPATH = "$.id";
 
@@ -82,6 +83,7 @@ public class SparkUpdateEntity {
 
                     JavaRDD<String> map = entitiesWithId.leftOuterJoin(mergedIds).map(k -> k._2()._2().isPresent() ? updateDeletedByInference(k._2()._1(), getOafClass(entity)) : k._2()._1());
                     sourceEntity = map.union(dedupEntity);
+
                 }
 
                 sourceEntity.saveAsTextFile(dedupGraphPath + "/" + entity, GzipCodec.class);

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

@@ -4,14 +4,6 @@
             <name>graphBasePath</name>
             <description>the raw graph base path</description>
         </property>
-        <property>
-            <name>isLookUpUrl</name>
-            <description>the address of the lookUp service</description>
-        </property>
-        <property>
-            <name>actionSetId</name>
-            <description>id of the actionSet</description>
-        </property>
         <property>
             <name>workingPath</name>
             <description>path of the working directory</description>
@@ -34,6 +26,21 @@
         </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>
+        </configuration>
+    </global>
+
     <start to="UpdateEntity"/>
 
     <kill name="Kill">
@@ -45,11 +52,9 @@
             <prepare>
                 <delete path='${dedupGraphPath}'/>
             </prepare>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <master>yarn-cluster</master>
             <mode>cluster</mode>
-            <name>Create Dedup Record</name>
+            <name>Update Entity</name>
             <class>eu.dnetlib.dhp.dedup.SparkUpdateEntity</class>
             <jar>dhp-dedup-${projectVersion}.jar</jar>
             <spark-opts>
@@ -74,8 +79,6 @@
             <prepare>
                 <delete path='${dedupGraphPath}/relation'/>
             </prepare>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
             <master>yarn-cluster</master>
             <mode>cluster</mode>
             <name>Update Relations</name>

dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/createCC_parameters.json

@@ -17,12 +17,6 @@
     "paramDescription": "the base path of the raw graph",
     "paramRequired": true
   },
-  {
-    "paramName": "o",
-    "paramLongName": "rawSet",
-    "paramDescription": "the raw set to be saved (full path)",
-    "paramRequired": true
-  },
   {
     "paramName": "la",
     "paramLongName": "isLookUpUrl",

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

@@ -27,7 +27,7 @@
     "paramName": "o",
     "paramLongName": "rawSet",
     "paramDescription": "the raw set to be saved (full path)",
-    "paramRequired": true
+    "paramRequired": false
   },
   {
     "paramName": "w",

dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/roots/oozie_app/config-default.xml

@@ -1,18 +0,0 @@
-<configuration>
-    <property>
-        <name>jobTracker</name>
-        <value>yarnRM</value>
-    </property>
-    <property>
-        <name>nameNode</name>
-        <value>hdfs://nameservice1</value>
-    </property>
-    <property>
-        <name>oozie.use.system.libpath</name>
-        <value>true</value>
-    </property>
-    <property>
-        <name>oozie.action.sharelib.for.spark</name>
-        <value>spark2</value>
-    </property>
-</configuration>

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

@@ -1,115 +0,0 @@
-<workflow-app name="Build Root Records" xmlns="uri:oozie:workflow:0.5">
-    <parameters>
-        <property>
-            <name>graphBasePath</name>
-            <description>the raw graph base path</description>
-        </property>
-        <property>
-            <name>isLookUpUrl</name>
-            <description>the address of the lookUp service</description>
-        </property>
-        <property>
-            <name>actionSetId</name>
-            <description>id of the actionSet</description>
-        </property>
-        <property>
-            <name>workingPath</name>
-            <description>path of the working directory</description>
-        </property>
-        <property>
-            <name>dedupGraphPath</name>
-            <description>path of the dedup graph</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>
-
-    <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>
-        </configuration>
-    </global>
-
-    <start to="CreateMergeRel"/>
-
-    <kill name="Kill">
-        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
-    </kill>
-
-    <action name="CreateMergeRel">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
-                <delete path='${workingPath}/${actionSetId}/*_mergerel'/>
-            </prepare>
-            <master>yarn-cluster</master>
-            <mode>cluster</mode>
-            <name>Create Merge Relations</name>
-            <class>eu.dnetlib.dhp.dedup.SparkCreateConnectedComponent</class>
-            <jar>dhp-dedup-${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>--i</arg><arg>${graphBasePath}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
-            <arg>--la</arg><arg>${isLookUpUrl}</arg>
-            <arg>--asi</arg><arg>${actionSetId}</arg>
-        </spark>
-        <ok to="CreateDedupRecord"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="CreateDedupRecord">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
-                <delete path='${workingPath}/${actionSetId}/*_deduprecord'/>
-            </prepare>
-            <master>yarn-cluster</master>
-            <mode>cluster</mode>
-            <name>Create Dedup Record</name>
-            <class>eu.dnetlib.dhp.dedup.SparkCreateDedupRecord</class>
-            <jar>dhp-dedup-${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>--i</arg><arg>${graphBasePath}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
-            <arg>--la</arg><arg>${isLookUpUrl}</arg>
-            <arg>--asi</arg><arg>${actionSetId}</arg>
-        </spark>
-        <ok to="End"/>
-        <error to="Kill"/>
-    </action>
-
-    <end name="End"/>
-</workflow-app>

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

@@ -1,4 +1,4 @@
-<workflow-app name="Create Similarity Relations" xmlns="uri:oozie:workflow:0.5">
+<workflow-app name="Duplicate Scan" xmlns="uri:oozie:workflow:0.5">
     <parameters>
         <property>
             <name>graphBasePath</name>
@@ -49,13 +49,13 @@
         </configuration>
     </global>
 
-    <start to="DuplicateScan"/>
+    <start to="CreateSimRel"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
-    <action name="DuplicateScan">
+    <action name="CreateSimRel">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <prepare>
                 <delete path="${rawSet}"/>
@@ -75,11 +75,66 @@
             </spark-opts>
             <arg>-mt</arg><arg>yarn</arg>
             <arg>--i</arg><arg>${graphBasePath}</arg>
-            <arg>--o</arg><arg>${rawSet}</arg>
             <arg>--la</arg><arg>${isLookUpUrl}</arg>
             <arg>--asi</arg><arg>${actionSetId}</arg>
             <arg>--w</arg><arg>${workingPath}</arg>
         </spark>
+        <ok to="CreateMergeRel"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="CreateMergeRel">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <prepare>
+                <delete path='${workingPath}/${actionSetId}/*_mergerel'/>
+            </prepare>
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Create Merge Relations</name>
+            <class>eu.dnetlib.dhp.dedup.SparkCreateConnectedComponent</class>
+            <jar>dhp-dedup-${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>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--la</arg><arg>${isLookUpUrl}</arg>
+            <arg>--asi</arg><arg>${actionSetId}</arg>
+        </spark>
+        <ok to="CreateDedupRecord"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="CreateDedupRecord">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <prepare>
+                <delete path='${workingPath}/${actionSetId}/*_deduprecord'/>
+            </prepare>
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Create Dedup Record</name>
+            <class>eu.dnetlib.dhp.dedup.SparkCreateDedupRecord</class>
+            <jar>dhp-dedup-${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>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--la</arg><arg>${isLookUpUrl}</arg>
+            <arg>--asi</arg><arg>${actionSetId}</arg>
+        </spark>
         <ok to="End"/>
         <error to="Kill"/>
     </action>

dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dhp/dedup/SparkCreateDedupTest.java

@@ -25,17 +25,14 @@ public class SparkCreateDedupTest {
 
     @Test
     @Ignore
-    public void createSimRelsTest2() throws Exception {
+    public void createSimRelsTest() throws Exception {
         SparkCreateSimRels.main(new String[]{
                 "-mt", "local[*]",
-                "-s", "/Users/miconis/dumps",
+                "-i", "/Users/miconis/dumps",
-                "-e", entity,
+                "-o", "/tmp/dedup/rawset_test",
-                "-c", ArgumentApplicationParser.compressArgument(configuration),
-                "-rs", "/tmp/dedup/rawset_test",
-                "-ai", "agentId",
-                "-an", "agentName",
                 "-asi", "dedup-similarity-result-levenstein",
                 "-la", "lookupurl",
+                "-w", "workingPath"
         });
     }