[Affilaition Propagation] moved the selection of graph relation as a preparation step

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/PrepareInfo.java

@@ -73,6 +73,9 @@ public class PrepareInfo implements Serializable {
 		final String resultOrganizationPath = parser.get("resultOrgPath");
 		log.info("resultOrganizationPath: {}", resultOrganizationPath);
 
+		final String relationPath = parser.get("relationPath");
+		log.info("relationPath: {}", relationPath);
+
 		SparkConf conf = new SparkConf();
 		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
 
@@ -84,11 +87,12 @@ public class PrepareInfo implements Serializable {
 				graphPath,
 				childParentPath,
 				leavesPath,
-				resultOrganizationPath));
+				resultOrganizationPath,
+					relationPath));
 	}
 
 	private static void prepareInfo(SparkSession spark, String inputPath, String childParentOrganizationPath,
-		String currentIterationPath, String resultOrganizationPath) {
+		String currentIterationPath, String resultOrganizationPath, String relationPath) {
 		Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class);
 		relation.createOrReplaceTempView("relation");
 
@@ -108,6 +112,15 @@ public class PrepareInfo implements Serializable {
 			.option("compression", "gzip")
 			.json(resultOrganizationPath);
 
+		relation
+				.filter(
+						(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
+								r.getRelClass().equals(ModelConstants.HAS_AUTHOR_INSTITUTION))
+				.write()
+				.mode(SaveMode.Overwrite)
+				.option("compression","gzip")
+				.json(relationPath);
+
 		Dataset<String> children = spark
 			.sql(
 				"Select distinct target as child from relation where " +

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/SparkResultToOrganizationFromSemRel.java

@@ -49,8 +49,8 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
 		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-		String graphPath = parser.get("graphPath");
+		String relationPath = parser.get("relationPath");
-		log.info("graphPath: {}", graphPath);
+		log.info("relationPath: {}", relationPath);
 
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
@@ -78,7 +78,7 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
 				leavesPath,
 				childParentPath,
 				resultOrganizationPath,
-				graphPath,
+				relationPath,
 				workingPath,
 				outputPath));
 	}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/StepActions.java

@@ -26,16 +26,11 @@ import scala.Tuple2;
 
 public class StepActions implements Serializable {
 
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
 	public static void execStep(SparkSession spark,
 		String graphPath, String newRelationPath,
 		String leavesPath, String chldParentOrgPath, String resultOrgPath) {
 
-		Dataset<Relation> relationGraph = readPath(spark, graphPath + "/relation", Relation.class)
+		Dataset<Relation> relationGraph = readPath(spark, graphPath, Relation.class);
-			.filter(
-				(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
-					r.getRelClass().equals(ModelConstants.HAS_AUTHOR_INSTITUTION));
 		// select only the relation source target among those proposed by propagation that are not already existent
 		getNewRels(
 			newRelationPath, relationGraph,
@@ -80,8 +75,8 @@ public class StepActions implements Serializable {
 				ret.setValueSet(orgs);
 				return ret;
 			}, Encoders.bean(KeyValueSet.class))
-			.write()
+				.write()
-			.mode(SaveMode.Overwrite)
+					.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
 			.json(outputPath);
 	}
@@ -116,7 +111,7 @@ public class StepActions implements Serializable {
 		// union of new propagation relations to the relation set
 		// grouping from sourcetarget (we are sure the only relations are those from result to organization by
 		// construction of the set)
-		// if at least one relation in the set was harvested no new relation will be returned
+		// if at least one relation in the set was not produced by propagation no new relation will be returned
 
 		relationDataset
 			.union(newRels)

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_preparation_parameter.json

@@ -34,5 +34,11 @@
     "paramLongName": "isSparkSessionManaged",
     "paramDescription": "the path where prepared info have been stored",
     "paramRequired": false
+  },
+  {
+    "paramName": "rep",
+    "paramLongName": "relationPath",
+    "paramDescription": "the path where to store the selected subset of relations",
+    "paramRequired": false
   }
 ]

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_propagation_parameter.json

@@ -1,7 +1,7 @@
 [
   {
-    "paramName":"gp",
+    "paramName":"rep",
-    "paramLongName":"graphPath",
+    "paramLongName":"relationPath",
     "paramDescription": "the path of the sequencial file to read",
     "paramRequired": true
   },

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml

@@ -150,6 +150,7 @@
             <arg>--leavesPath</arg><arg>${workingDir}/preparedInfo/leavesPath</arg>
             <arg>--childParentPath</arg><arg>${workingDir}/preparedInfo/childParentPath</arg>
             <arg>--resultOrgPath</arg><arg>${workingDir}/preparedInfo/resultOrgPath</arg>
+            <arg>--relationPath</arg><arg>${workingDir}/preparedInfo/relation</arg>
         </spark>
         <ok to="apply_resulttoorganization_propagation"/>
         <error to="Kill"/>
@@ -173,7 +174,7 @@
                 --conf spark.dynamicAllocation.enabled=true
                 --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
-            <arg>--graphPath</arg><arg>${sourcePath}</arg>
+            <arg>--relationPath</arg><arg>${workingDir}/preparedInfo/relation</arg>
             <arg>--outputPath</arg><arg>${outputPath}/relation</arg>
             <arg>--leavesPath</arg><arg>${workingDir}/preparedInfo/leavesPath</arg>
             <arg>--childParentPath</arg><arg>${workingDir}/preparedInfo/childParentPath</arg>

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/PrepareInfoJobTest.java

@@ -84,6 +84,7 @@ public class PrepareInfoJobTest {
 					"-leavesPath", workingDir.toString() + "/currentIteration/",
 					"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
 					"-childParentPath", workingDir.toString() + "/childParentOrg/",
+						"-relationPath", workingDir.toString() + "/relation"
 
 				});
 
@@ -228,6 +229,7 @@ public class PrepareInfoJobTest {
 					"-leavesPath", workingDir.toString() + "/currentIteration/",
 					"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
 					"-childParentPath", workingDir.toString() + "/childParentOrg/",
+						"-relationPath", workingDir.toString() + "/relation"
 
 				});
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@@ -332,6 +334,35 @@ public class PrepareInfoJobTest {
 
 	}
 
+	@Test
+	public void relationTest()throws Exception {
+
+		PrepareInfo
+				.main(
+						new String[] {
+								"-isSparkSessionManaged", Boolean.FALSE.toString(),
+								"-graphPath", getClass()
+								.getResource(
+										"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest")
+								.getPath(),
+								"-hive_metastore_uris", "",
+								"-leavesPath", workingDir.toString() + "/currentIteration/",
+								"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
+								"-childParentPath", workingDir.toString() + "/childParentOrg/",
+								"-relationPath", workingDir.toString() + "/relation"
+
+						});
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+				.textFile(workingDir.toString() + "/relation")
+				.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
+
+		Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
+
+		Assertions.assertEquals(7, verificationDs.count());
+
+	}
 	@Test
 	public void resultOrganizationTest1() throws Exception {
 
@@ -347,6 +378,7 @@ public class PrepareInfoJobTest {
 					"-leavesPath", workingDir.toString() + "/currentIteration/",
 					"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
 					"-childParentPath", workingDir.toString() + "/childParentOrg/",
+						"-relationPath", workingDir.toString() + "/relation"
 
 				});
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@@ -467,10 +499,6 @@ public class PrepareInfoJobTest {
 
 	@Test
 	public void foundLeavesTest1() throws Exception {
-//		PrepareInfo.prepareInfo(spark, getClass()
-//				.getResource(
-//						"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest")
-//				.getPath(), workingDir.toString() + "/childParentOrg/", workingDir.toString() + "/currentIteration/",workingDir.toString() + "/resultOrganization/");
 
 		PrepareInfo
 			.main(
@@ -484,6 +512,7 @@ public class PrepareInfoJobTest {
 					"-leavesPath", workingDir.toString() + "/currentIteration/",
 					"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
 					"-childParentPath", workingDir.toString() + "/childParentOrg/",
+						"-relationPath", workingDir.toString() + "/relation"
 
 				});
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@@ -510,12 +539,9 @@ public class PrepareInfoJobTest {
 					"-leavesPath", workingDir.toString() + "/currentIteration/",
 					"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
 					"-childParentPath", workingDir.toString() + "/childParentOrg/",
+						"-relationPath", workingDir.toString() + "/relation"
 
 				});
-//		PrepareInfo.prepareInfo(spark, getClass()
-//				.getResource(
-//						"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/childparenttest1")
-//				.getPath(), workingDir.toString() + "/childParentOrg/", workingDir.toString() + "/currentIteration/",workingDir.toString() + "/resultOrganization/");
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/SparkJobTest.java

@@ -101,9 +101,9 @@ public class SparkJobTest {
 			.main(
 				new String[] {
 					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-graphPath", graphPath,
+					"-relationPath", graphPath,
 					"-hive_metastore_uris", "",
-					"-outputPath", workingDir.toString() + "/relation",
+					"-outputPath", workingDir.toString() + "/finalrelation",
 					"-leavesPath", workingDir.toString() + "/leavesInput",
 					"-resultOrgPath", workingDir.toString() + "/orgsInput",
 					"-childParentPath", childParentPath,
@@ -113,9 +113,11 @@ public class SparkJobTest {
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<Relation> tmp = sc
-			.textFile(workingDir.toString() + "/relation")
+			.textFile(workingDir.toString() + "/finalrelation")
 			.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
 
+		tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
+
 		Assertions.assertEquals(18, tmp.count());
 		tmp.foreach(r -> Assertions.assertEquals(ModelConstants.AFFILIATION, r.getSubRelType()));
 		tmp.foreach(r -> Assertions.assertEquals(ModelConstants.RESULT_ORGANIZATION, r.getRelType()));