updated baseline workflow

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala

@@ -45,6 +45,11 @@ object SparkCreateBaselineDataFrame {
     parser.parseArgument(args)
     val isLookupUrl: String = parser.get("isLookupUrl")
     log.info("isLookupUrl: {}", isLookupUrl)
+    val workingPath = parser.get("workingPath")
+    log.info("workingPath: {}", workingPath)
+
+    val targetPath = parser.get("targetPath")
+    log.info("targetPath: {}", targetPath)
 
     val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
     val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
@@ -59,7 +64,7 @@ object SparkCreateBaselineDataFrame {
 
     val sc = spark.sparkContext
 
-    val workingPath = parser.get("workingPath")
+
 
     implicit  val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
     implicit  val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
@@ -81,6 +86,8 @@ object SparkCreateBaselineDataFrame {
     exported_dataset
       .map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
       .filter(p => p!= null)
-      .write.mode(SaveMode.Overwrite).save(s"$workingPath/oaf/baseline_oaf")
+      .write.mode(SaveMode.Overwrite).save(targetPath)
+
+    //s"$workingPath/oaf/baseline_oaf"
   }
 }

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json

@@ -1,5 +1,6 @@
 [
   {"paramName":"mt",  "paramLongName":"master",     "paramDescription": "should be local or yarn",                  "paramRequired": true},
   {"paramName":"i",   "paramLongName":"isLookupUrl","paramDescription": "isLookupUrl",                              "paramRequired": true},
-  {"paramName":"w",   "paramLongName":"workingPath","paramDescription": "the path of the sequencial file to read",  "paramRequired": true}
+  {"paramName":"w",   "paramLongName":"workingPath","paramDescription": "the path of the sequencial file to read",  "paramRequired": true},
+  {"paramName":"t",   "paramLongName":"targetPath","paramDescription": "the oaf path ",                             "paramRequired": true}
 ]

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/workflow.xml

@@ -4,6 +4,10 @@
             <name>baselineWorkingPath</name>
             <description>the Baseline Working Path</description>
         </property>
+        <property>
+            <name>targetPath</name>
+            <description>the Target Path</description>
+        </property>
         <property>
             <name>isLookupUrl</name>
             <description>The IS lookUp service endopoint</description>
@@ -34,6 +38,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
             <arg>--workingPath</arg><arg>${baselineWorkingPath}</arg>
+            <arg>--targetPath</arg><arg>${targetPath}</arg>
             <arg>--master</arg><arg>yarn</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
         </spark>