From aa48d5270779fcdb3dfdc73cd7a9afc9cae47920 Mon Sep 17 00:00:00 2001
From: "miriam.baglioni" <miriam.baglioni@isti.cnr.it>
Date: Wed, 25 Oct 2023 15:18:44 +0200
Subject: [PATCH] fixing issues

---
 ...ExtendEoscResultWithOrganizationStep2.java | 36 ++++++++++---------
 .../oa/graph/dump/eosc/oozie_app/workflow.xml |  4 +++
 ...d_result_with_organization_parameters.json |  7 +++-
 3 files changed, 30 insertions(+), 17 deletions(-)

diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/ExtendEoscResultWithOrganizationStep2.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/ExtendEoscResultWithOrganizationStep2.java
index 1ca6f20..af4bb19 100644
--- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/ExtendEoscResultWithOrganizationStep2.java
+++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/ExtendEoscResultWithOrganizationStep2.java
@@ -63,6 +63,9 @@ public class ExtendEoscResultWithOrganizationStep2 implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
+		final String resultType = parser.get("resultType");
+		log.info("resultType: {}", resultType);
+
 		SparkConf conf = new SparkConf();
 
 		runWithSparkSession(
@@ -70,14 +73,14 @@ public class ExtendEoscResultWithOrganizationStep2 implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Utils.removeOutputDir(spark, workingPath + "publicationextendedaffiliation");
-				addOrganizations(spark, inputPath, workingPath, outputPath);
+				addOrganizations(spark, inputPath, workingPath, outputPath, resultType);
 			});
 	}
 
-	private static void addOrganizations(SparkSession spark, String inputPath, String workingPath, String outputPath) {
+	private static void addOrganizations(SparkSession spark, String inputPath, String workingPath, String outputPath, String resultType) {
 
 		Dataset<Result> results = Utils
-			.readPath(spark, workingPath + "publication", Result.class);
+			.readPath(spark, workingPath + "resultType", Result.class);
 
 		Dataset<Relation> relations = Utils
 			.readPath(spark, inputPath + "/relation", Relation.class)
@@ -155,20 +158,21 @@ public class ExtendEoscResultWithOrganizationStep2 implements Serializable {
 			.option("compression", "gzip")
 			.json(workingPath + "publicationextendedaffiliation");
 
-		relations
-			.joinWith(organizations, relations.col("source").equalTo(organizations.col("id")))
-			.map(
-				(MapFunction<Tuple2<Relation, Organization>, eu.dnetlib.dhp.eosc.model.Organization>) t2 -> mapOrganization(
-					t2._2()),
-				Encoders.bean(eu.dnetlib.dhp.eosc.model.Organization.class))
-			.filter(Objects::nonNull)
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(outputPath + "organization");
+		Dataset<Relation> organizationWithAffiliation = relations
+				.joinWith(results, relations.col("target").equalTo(results.col("id")))
+				.map((MapFunction<Tuple2<Relation, Result>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class));
 
-		relations
-			.joinWith(organizations, relations.col("source").equalTo(organizations.col("id")))
+		organizationWithAffiliation.joinWith(organizations, organizationWithAffiliation.col("source").equalTo(organizations.col("id")))
+				.map((MapFunction<Tuple2<Relation, Organization>, eu.dnetlib.dhp.eosc.model.Organization>) t2 -> mapOrganization(
+								t2._2()),
+						Encoders.bean(eu.dnetlib.dhp.eosc.model.Organization.class))
+				.filter(Objects::nonNull)
+				.write()
+				.mode(SaveMode.Overwrite)
+				.option("compression", "gzip")
+				.json(outputPath + "organization");
+
+		organizationWithAffiliation.joinWith(organizations, organizationWithAffiliation.col("source").equalTo(organizations.col("id")))
 			.map(
 				(MapFunction<Tuple2<Relation, Organization>, eu.dnetlib.dhp.eosc.model.Relation>) t2 -> eu.dnetlib.dhp.eosc.model.Relation
 					.newInstance(t2._1().getSource(), t2._1().getTarget()),
diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/eosc/oozie_app/workflow.xml b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/eosc/oozie_app/workflow.xml
index 077bb4f..fd1bcdc 100644
--- a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/eosc/oozie_app/workflow.xml
+++ b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/eosc/oozie_app/workflow.xml
@@ -166,6 +166,7 @@
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--workingPath</arg><arg>${workingDir}/dump/</arg>
             <arg>--outputPath</arg><arg>${outputPath}/dump/</arg>
+            <arg>--resultType</arg><arg>publication</arg>
         </spark>
         <ok to="wait_eosc_dump"/>
         <error to="Kill"/>
@@ -218,6 +219,7 @@
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--workingPath</arg><arg>${workingDir}/dump/</arg>
             <arg>--outputPath</arg><arg>${outputPath}/dump/</arg>
+            <arg>--resultType</arg><arg>dataset</arg>
         </spark>
         <ok to="wait_eosc_dump"/>
         <error to="Kill"/>
@@ -271,6 +273,7 @@
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--workingPath</arg><arg>${workingDir}/dump/</arg>
             <arg>--outputPath</arg><arg>${outputPath}/dump/</arg>
+            <arg>--resultType</arg><arg>otherresearchproduct</arg>
         </spark>
         <ok to="wait_eosc_dump"/>
         <error to="Kill"/>
@@ -323,6 +326,7 @@
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--workingPath</arg><arg>${workingDir}/dump/</arg>
             <arg>--outputPath</arg><arg>${outputPath}/dump/</arg>
+            <arg>--resultType</arg><arg>software</arg>
         </spark>
         <ok to="wait_eosc_dump"/>
         <error to="Kill"/>
diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/eosc_extend_result_with_organization_parameters.json b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/eosc_extend_result_with_organization_parameters.json
index 3a448b6..3bd3108 100644
--- a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/eosc_extend_result_with_organization_parameters.json
+++ b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/eosc_extend_result_with_organization_parameters.json
@@ -28,7 +28,12 @@
 	"paramLongName":"workingPath",
 	"paramDescription": "The path to the community map",
 	"paramRequired": false
-}
+},
+	{
+		"paramName":"rt",
+		"paramLongName":"resultType",
+		"paramDescription": "The path to the community map",
+		"paramRequired": false}
 ]