From 62cc257e5c2b18574e78e51ea7c13be3c7031714 Mon Sep 17 00:00:00 2001
From: Sandro La Bruzzo <sandro.labruzzo@isti.cnr.it>
Date: Fri, 27 Mar 2020 17:07:34 +0100
Subject: [PATCH] fixed step1 workflow

---
 dhp-workflows/dhp-dedup-scholexplorer/pom.xml | 31 ++++++++++
 dhp-workflows/dhp-graph-mapper/README.md      |  3 +
 .../dhp/sx/graph/step1/oozie_app/workflow.xml | 59 ++++++++++++++++---
 3 files changed, 85 insertions(+), 8 deletions(-)
 create mode 100644 dhp-workflows/dhp-graph-mapper/README.md

diff --git a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml
index f1b51a7094..387952e338 100644
--- a/dhp-workflows/dhp-dedup-scholexplorer/pom.xml
+++ b/dhp-workflows/dhp-dedup-scholexplorer/pom.xml
@@ -10,6 +10,37 @@
 
     <artifactId>dhp-dedup-scholexplorer</artifactId>
 
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>net.alchim31.maven</groupId>
+                <artifactId>scala-maven-plugin</artifactId>
+                <version>4.0.1</version>
+                <executions>
+                    <execution>
+                        <id>scala-compile-first</id>
+                        <phase>initialize</phase>
+                        <goals>
+                            <goal>add-source</goal>
+                            <goal>compile</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>scala-test-compile</id>
+                        <phase>process-test-resources</phase>
+                        <goals>
+                            <goal>testCompile</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <configuration>
+                    <scalaVersion>${scala.version}</scalaVersion>
+                </configuration>
+            </plugin>
+        </plugins>
+
+    </build>
+
     <dependencies>
 
         <dependency>
diff --git a/dhp-workflows/dhp-graph-mapper/README.md b/dhp-workflows/dhp-graph-mapper/README.md
new file mode 100644
index 0000000000..8105197b47
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/README.md
@@ -0,0 +1,3 @@
+# dnet-graph-mapper
+Dnet-graph-mapper is a DNET module responsible 
+of importing the first version of graph into Hadoop Cluster. 
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml
index 4da737c336..ce00eff7b3 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml
@@ -1,11 +1,20 @@
 <workflow-app name="Create Raw Graph Step 1: import Entities from aggregator to HDFS" 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>workingPath</name>
             <description>the working dir base path</description>
         </property>
         <property>
-            <name>targetPath</name>
+            <name>targetXMLPath</name>
+            <description>the graph Raw base path</description>
+        </property>
+        <property>
+            <name>targetEntityPath</name>
             <description>the graph Raw base path</description>
         </property>
         <property>
@@ -29,12 +38,20 @@
             <description>mongo database</description>
         </property>
         <property>
-            <name>user</name>
-            <description>HDFS user</description>
+            <name>entity</name>
+            <description>the entity type</description>
         </property>
     </parameters>
 
-    <start to="ResetWorkingPath"/>
+    <start to="ReuseContent"/>
+
+    <decision name="ReuseContent">
+        <switch>
+            <case to="ResetWorkingPath">${wf:conf('reuseContent') eq false}</case>
+            <case to="ResetTargetPath">${wf:conf('reuseContent') eq true}</case>
+            <default to="ResetWorkingPath"/>
+        </switch>
+    </decision>
 
 
     <kill name="Kill">
@@ -43,8 +60,8 @@
 
     <action name="ResetWorkingPath">
         <fs>
-            <delete path='${targetPath}'/>
-            <mkdir path='${workingPath}'/>
+            <delete path='${workingPath}'/>
+            <mkdir path='${workingPath}/input'/>
         </fs>
         <ok to="ImportEntitiesFromMongo"/>
         <error to="Kill"/>
@@ -56,9 +73,8 @@
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <main-class>eu.dnetlib.dhp.sx.graph.ImportDataFromMongo</main-class>
-            <arg>-t</arg><arg>${targetPath}</arg>
+            <arg>-t</arg><arg>${targetXMLPath}</arg>
             <arg>-n</arg><arg>${nameNode}</arg>
-            <arg>-u</arg><arg>${user}</arg>
             <arg>-h</arg><arg>${dbhost}</arg>
             <arg>-p</arg><arg>27017</arg>
             <arg>-dn</arg><arg>${dbName}</arg>
@@ -66,6 +82,33 @@
             <arg>-l</arg><arg>${layout}</arg>
             <arg>-i</arg><arg>${interpretation}</arg>
         </java>
+        <ok to="ResetTargetPath"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ResetTargetPath">
+        <fs>
+            <delete path='${targetEntityPath}'/>
+        </fs>
+        <ok to="ConvertXML2Entity"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ConvertXML2Entity">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Import ${entity} and related entities</name>
+            <class>eu.dnetlib.dhp.sx.graph.SparkScholexplorerGraphImporter</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
+            <arg>-mt</arg> <arg>yarn-cluster</arg>
+            <arg>--sourcePath</arg><arg>${targetXMLPath}</arg>
+            <arg>--targetPath</arg><arg>${targetEntityPath}</arg>
+            <arg>--entity</arg><arg>${entity}</arg>
+        </spark>
         <ok to="End"/>
         <error to="Kill"/>
     </action>