diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala
index b9cccf4e1..26efd723f 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala
+++ b/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"
}
}
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json
index 4899fa76d..38eb50094 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json
+++ b/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}
]
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/workflow.xml
index 63abba24e..914d1c2c7 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/workflow.xml
@@ -4,6 +4,10 @@
baselineWorkingPath
the Baseline Working Path
+
+ targetPath
+ the Target Path
+
isLookupUrl
The IS lookUp service endopoint
@@ -34,6 +38,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--workingPath${baselineWorkingPath}
+ --targetPath${targetPath}
--masteryarn
--isLookupUrl${isLookupUrl}