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}