-

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java

@@ -1,10 +1,14 @@
 package eu.dnetlib.dhp.resulttocommunityfromsemrel;
 
+import static eu.dnetlib.dhp.PropagationConstant.*;
+
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.QueryInformationSystem;
 import eu.dnetlib.dhp.TypedRow;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.*;
+import java.util.*;
+import java.util.stream.Collectors;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.spark.SparkConf;
@@ -16,28 +20,24 @@ import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import scala.Tuple2;
 
-import java.util.*;
-import java.util.stream.Collectors;
-
-import static eu.dnetlib.dhp.PropagationConstant.*;
-
 public class SparkResultToCommunityThroughSemRelJob {
     public static void main(String[] args) throws Exception {
 
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils
-                .toString(SparkResultToCommunityThroughSemRelJob.class
-                        .getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_propagationresultcommunityfromsemrel_parameters.json")));
+        final ArgumentApplicationParser parser =
+                new ArgumentApplicationParser(
+                        IOUtils.toString(
+                                SparkResultToCommunityThroughSemRelJob.class.getResourceAsStream(
+                                        "/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")));
         parser.parseArgument(args);
 
         for (String key : parser.getObjectMap().keySet()) {
             System.out.println(key + " = " + parser.get(key));
         }
 
-
         SparkConf conf = new SparkConf();
         conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
-        final SparkSession spark = SparkSession
-                .builder()
+        final SparkSession spark =
+                SparkSession.builder()
                         .appName(SparkResultToCommunityThroughSemRelJob.class.getSimpleName())
                         .master(parser.get("master"))
                         .config(conf)
@@ -48,56 +48,74 @@ public class SparkResultToCommunityThroughSemRelJob {
         final String inputPath = parser.get("sourcePath");
         final String outputPath = "/tmp/provision/propagation/resulttocommunityfromsemrel";
 
-        //final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
+        // final List<String> allowedsemrel =
+        // Arrays.asList(parser.get("allowedsemrels").split(";"));
         final List<String> allowedsemrel = Arrays.asList("isSupplementedBy", "isSupplementTo");
-        //final List<String> communityIdList = QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
-        final List<String> communityIdList = QueryInformationSystem.getCommunityList("http://beta.services.openaire.eu:8280/is/services/isLookUp");
+        // final List<String> communityIdList =
+        // QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
+        final List<String> communityIdList =
+                QueryInformationSystem.getCommunityList(
+                        "http://beta.services.openaire.eu:8280/is/services/isLookUp");
 
         createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
 
-
-        JavaRDD<Publication> all_publication_rdd = sc.textFile(inputPath + "/publication")
+        JavaRDD<Publication> all_publication_rdd =
+                sc.textFile(inputPath + "/publication")
                         .map(item -> new ObjectMapper().readValue(item, Publication.class))
-                .filter(p -> !p.getDataInfo().getDeletedbyinference()).cache();
-        JavaRDD<Publication> publication_rdd = all_publication_rdd
-                .filter(p -> relatedToCommunities(p, communityIdList)).cache();
+                        .filter(p -> !p.getDataInfo().getDeletedbyinference())
+                        .cache();
+        JavaRDD<Publication> publication_rdd =
+                all_publication_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
 
-        JavaRDD<Dataset> all_dataset_rdd = sc.textFile(inputPath + "/dataset")
+        JavaRDD<Dataset> all_dataset_rdd =
+                sc.textFile(inputPath + "/dataset")
                         .map(item -> new ObjectMapper().readValue(item, Dataset.class))
-                .filter(p -> !p.getDataInfo().getDeletedbyinference()).cache();
-        JavaRDD<Dataset> dataset_rdd = all_dataset_rdd
-                .filter(p -> relatedToCommunities(p, communityIdList)).cache();
+                        .filter(p -> !p.getDataInfo().getDeletedbyinference())
+                        .cache();
+        JavaRDD<Dataset> dataset_rdd =
+                all_dataset_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
 
-        JavaRDD<OtherResearchProduct> all_orp_rdd = sc.textFile(inputPath + "/otherresearchproduct")
+        JavaRDD<OtherResearchProduct> all_orp_rdd =
+                sc.textFile(inputPath + "/otherresearchproduct")
                         .map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class))
-                .filter(p -> !p.getDataInfo().getDeletedbyinference()).cache();
-        JavaRDD<OtherResearchProduct> orp_rdd = all_orp_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
+                        .filter(p -> !p.getDataInfo().getDeletedbyinference())
+                        .cache();
+        JavaRDD<OtherResearchProduct> orp_rdd =
+                all_orp_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
 
-        JavaRDD<Software> all_software_rdd = sc.textFile(inputPath + "/software")
+        JavaRDD<Software> all_software_rdd =
+                sc.textFile(inputPath + "/software")
                         .map(item -> new ObjectMapper().readValue(item, Software.class))
-                .filter(p -> !p.getDataInfo().getDeletedbyinference()).cache();
-        JavaRDD<Software> software_rdd = all_software_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
+                        .filter(p -> !p.getDataInfo().getDeletedbyinference())
+                        .cache();
+        JavaRDD<Software> software_rdd =
+                all_software_rdd.filter(p -> relatedToCommunities(p, communityIdList)).cache();
 
-        JavaRDD<Relation> relation_rdd = sc.textFile(inputPath + "/relation")
+        JavaRDD<Relation> relation_rdd =
+                sc.textFile(inputPath + "/relation")
                         .map(item -> new ObjectMapper().readValue(item, Relation.class))
                         .filter(r -> !r.getDataInfo().getDeletedbyinference())
-                .filter(r -> allowedsemrel.contains(r.getRelClass()) && RELATION_RESULTRESULT_REL_TYPE.equals(r.getRelType())).cache();
+                        .filter(
+                                r ->
+                                        allowedsemrel.contains(r.getRelClass())
+                                                && RELATION_RESULTRESULT_REL_TYPE.equals(
+                                                        r.getRelType()))
+                        .cache();
 
+        org.apache.spark.sql.Dataset<Publication> publication =
+                spark.createDataset(publication_rdd.rdd(), Encoders.bean(Publication.class));
 
-        org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(publication_rdd.rdd(),
-                Encoders.bean(Publication.class));
+        org.apache.spark.sql.Dataset<Dataset> dataset =
+                spark.createDataset(dataset_rdd.rdd(), Encoders.bean(Dataset.class));
 
-        org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(dataset_rdd.rdd(),
-                Encoders.bean(Dataset.class));
+        org.apache.spark.sql.Dataset<OtherResearchProduct> other =
+                spark.createDataset(orp_rdd.rdd(), Encoders.bean(OtherResearchProduct.class));
 
-        org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(orp_rdd.rdd(),
-                Encoders.bean(OtherResearchProduct.class));
+        org.apache.spark.sql.Dataset<Software> software =
+                spark.createDataset(software_rdd.rdd(), Encoders.bean(Software.class));
 
-        org.apache.spark.sql.Dataset<Software> software = spark.createDataset(software_rdd.rdd(),
-                Encoders.bean(Software.class));
-
-        org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(relation_rdd.rdd(),
-                Encoders.bean(Relation.class));
+        org.apache.spark.sql.Dataset<Relation> relation =
+                spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
 
         publication.createOrReplaceTempView("publication");
         relation.createOrReplaceTempView("relation");
@@ -105,14 +123,17 @@ public class SparkResultToCommunityThroughSemRelJob {
         software.createOrReplaceTempView("software");
         other.createOrReplaceTempView("other");
 
-//        org.apache.spark.sql.Dataset<Row> publication_context = getContext(spark, "publication");
+        //        org.apache.spark.sql.Dataset<Row> publication_context = getContext(spark,
+        // "publication");
         //        publication_context.createOrReplaceTempView("publication_context");
 
-        org.apache.spark.sql.Dataset<Row> publication_context = spark.sql( "SELECT relation.source, " +
-                "publication.context , relation.target " +
-                "FROM publication " +
-                " JOIN relation  " +
-                "ON  id = source");
+        org.apache.spark.sql.Dataset<Row> publication_context =
+                spark.sql(
+                        "SELECT relation.source, "
+                                + "publication.context , relation.target "
+                                + "FROM publication "
+                                + " JOIN relation  "
+                                + "ON  id = source");
 
         org.apache.spark.sql.Dataset<Row> dataset_context = getContext(spark, "dataset");
         dataset_context.createOrReplaceTempView("dataset_context");
@@ -123,53 +144,95 @@ public class SparkResultToCommunityThroughSemRelJob {
         org.apache.spark.sql.Dataset<Row> other_context = getContext(spark, "other");
         other_context.createOrReplaceTempView("other_context");
 
-        publication = spark.createDataset(all_publication_rdd.rdd(),
-                Encoders.bean(Publication.class));
+        publication =
+                spark.createDataset(all_publication_rdd.rdd(), Encoders.bean(Publication.class));
         publication.createOrReplaceTempView("publication");
 
-        dataset = spark.createDataset(all_dataset_rdd.rdd(),
-                Encoders.bean(Dataset.class));
+        dataset = spark.createDataset(all_dataset_rdd.rdd(), Encoders.bean(Dataset.class));
         dataset.createOrReplaceTempView("dataset");
 
-        other = spark.createDataset(all_orp_rdd.rdd(),
-                Encoders.bean(OtherResearchProduct.class));
+        other = spark.createDataset(all_orp_rdd.rdd(), Encoders.bean(OtherResearchProduct.class));
         other.createOrReplaceTempView("other");
 
-        software = spark.createDataset(all_software_rdd.rdd(),
-                Encoders.bean(Software.class));
+        software = spark.createDataset(all_software_rdd.rdd(), Encoders.bean(Software.class));
         software.createOrReplaceTempView("software");
 
+        org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult =
+                getUpdateCommunitiesForTable(spark, "software");
+        org.apache.spark.sql.Dataset<Row> toupdatedatasetresult =
+                getUpdateCommunitiesForTable(spark, "dataset");
+        org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult =
+                getUpdateCommunitiesForTable(spark, "publication");
+        org.apache.spark.sql.Dataset<Row> toupdateotherresult =
+                getUpdateCommunitiesForTable(spark, "other");
 
-        org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult = getUpdateCommunitiesForTable(spark, "software");
-        org.apache.spark.sql.Dataset<Row> toupdatedatasetresult = getUpdateCommunitiesForTable(spark, "dataset");
-        org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult = getUpdateCommunitiesForTable(spark, "publication");
-        org.apache.spark.sql.Dataset<Row> toupdateotherresult = getUpdateCommunitiesForTable(spark, "other");
+        createUpdateForResultDatasetWrite(
+                toupdatesoftwareresult.toJavaRDD(),
+                outputPath,
+                "software_update",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        createUpdateForResultDatasetWrite(toupdatesoftwareresult.toJavaRDD(), outputPath, "software_update",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        createUpdateForResultDatasetWrite(
+                toupdatedatasetresult.toJavaRDD(),
+                outputPath,
+                "dataset_update",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        createUpdateForResultDatasetWrite(toupdatedatasetresult.toJavaRDD(),  outputPath, "dataset_update",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        createUpdateForResultDatasetWrite(
+                toupdatepublicationreresult.toJavaRDD(),
+                outputPath,
+                "publication_update",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        createUpdateForResultDatasetWrite(toupdatepublicationreresult.toJavaRDD(),  outputPath, "publication_update",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        createUpdateForResultDatasetWrite(
+                toupdateotherresult.toJavaRDD(),
+                outputPath,
+                "other_update",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        createUpdateForResultDatasetWrite(toupdateotherresult.toJavaRDD(), outputPath, "other_update",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        updateForDatasetDataset(
+                toupdatedatasetresult.toJavaRDD(),
+                dataset.toJavaRDD(),
+                outputPath,
+                "dataset",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
+        updateForOtherDataset(
+                toupdateotherresult.toJavaRDD(),
+                other.toJavaRDD(),
+                outputPath,
+                "otherresearchproduct",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        updateForDatasetDataset(toupdatedatasetresult.toJavaRDD(), dataset.toJavaRDD(), outputPath, "dataset",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
-
-        updateForOtherDataset(toupdateotherresult.toJavaRDD(), other.toJavaRDD(), outputPath, "otherresearchproduct",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
-
-        updateForSoftwareDataset(toupdatesoftwareresult.toJavaRDD(), software.toJavaRDD(), outputPath, "software",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
-
-        updateForPublicationDataset(toupdatepublicationreresult.toJavaRDD(), publication.toJavaRDD(), outputPath, "publication",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        updateForSoftwareDataset(
+                toupdatesoftwareresult.toJavaRDD(),
+                software.toJavaRDD(),
+                outputPath,
+                "software",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
+        updateForPublicationDataset(
+                toupdatepublicationreresult.toJavaRDD(),
+                publication.toJavaRDD(),
+                outputPath,
+                "publication",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
         /*
                 JavaPairRDD<String, TypedRow> resultLinkedToCommunities = publication
@@ -209,45 +272,67 @@ public class SparkResultToCommunityThroughSemRelJob {
         */
     }
 
-   private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(SparkSession spark, String table){
-        String query = "SELECT target_id, collect_set(co.id) context_id  " +
-                "       FROM (SELECT t.id target_id, s.context source_context " +
-                "             FROM context_software s " +
-                "             JOIN " + table + " t " +
-                "             ON s.target = t.id " +
-                "             UNION ALL " +
-                "             SELECT t.id target_id, d.context source_context " +
-                "             FROM dataset_context d  " +
-                "             JOIN " + table + " t" +
-                "             ON s.target = t.id  " +
-                "             UNION ALL  " +
-                "             SELECT t.id target_id, p.context source_context " +
-                "             FROM publication_context p" +
-                "             JOIN " + table +" t " +
-                "             on p.target = t.id " +
-                "             UNION ALL " +
-                "             SELECT t.id target_id, o.context source_context " +
-                "             FROM other_context o " +
-                "             JOIN " + table + " t  " +
-                "             ON o.target = t.id)  TMP " +
-                "             LATERAL VIEW EXPLODE(source_context) MyT as co " +
-                "             GROUP BY target_id" ;
+    private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(
+            SparkSession spark, String table) {
+        String query =
+                "SELECT target_id, collect_set(co.id) context_id  "
+                        + "       FROM (SELECT t.id target_id, s.context source_context "
+                        + "             FROM context_software s "
+                        + "             JOIN "
+                        + table
+                        + " t "
+                        + "             ON s.target = t.id "
+                        + "             UNION ALL "
+                        + "             SELECT t.id target_id, d.context source_context "
+                        + "             FROM dataset_context d  "
+                        + "             JOIN "
+                        + table
+                        + " t"
+                        + "             ON s.target = t.id  "
+                        + "             UNION ALL  "
+                        + "             SELECT t.id target_id, p.context source_context "
+                        + "             FROM publication_context p"
+                        + "             JOIN "
+                        + table
+                        + " t "
+                        + "             on p.target = t.id "
+                        + "             UNION ALL "
+                        + "             SELECT t.id target_id, o.context source_context "
+                        + "             FROM other_context o "
+                        + "             JOIN "
+                        + table
+                        + " t  "
+                        + "             ON o.target = t.id)  TMP "
+                        + "             LATERAL VIEW EXPLODE(source_context) MyT as co "
+                        + "             GROUP BY target_id";
 
         return spark.sql(query);
     }
 
-    private static JavaRDD<Result> createUpdateForResultDatasetWrite(JavaRDD<Row> toupdateresult, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
-        return toupdateresult.map(r -> {
+    private static JavaRDD<Result> createUpdateForResultDatasetWrite(
+            JavaRDD<Row> toupdateresult,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
+        return toupdateresult
+                .map(
+                        r -> {
                             List<Context> contextList = new ArrayList();
                             List<String> toAddContext = r.getList(1);
                             for (String cId : toAddContext) {
                                 if (communityIdList.contains(cId)) {
                                     Context newContext = new Context();
                                     newContext.setId(cId);
-                    newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+                                    newContext.setDataInfo(
+                                            Arrays.asList(
+                                                    getDataInfo(
+                                                            PROPAGATION_DATA_INFO_TYPE,
+                                                            class_id,
+                                                            class_name)));
                                     contextList.add(newContext);
                                 }
-
                             }
 
                             if (contextList.size() > 0) {
@@ -257,46 +342,110 @@ public class SparkResultToCommunityThroughSemRelJob {
                                 return ret;
                             }
                             return null;
-        }).filter(r -> r != null);
+                        })
+                .filter(r -> r != null);
     }
 
-    private static void updateForSoftwareDataset(JavaRDD<Row> toupdateresult, JavaRDD<Software> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForSoftwareDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<Software> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (Software) r)
                 .map(s -> new ObjectMapper().writeValueAsString(s))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-    private static void updateForDatasetDataset(JavaRDD<Row> toupdateresult, JavaRDD<Dataset> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForDatasetDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<Dataset> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (Dataset) r)
                 .map(d -> new ObjectMapper().writeValueAsString(d))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-    private static void updateForPublicationDataset(JavaRDD<Row> toupdateresult, JavaRDD<Publication> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForPublicationDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<Publication> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (Publication) r)
                 .map(p -> new ObjectMapper().writeValueAsString(p))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-    private static void updateForOtherDataset(JavaRDD<Row> toupdateresult, JavaRDD<OtherResearchProduct> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForOtherDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<OtherResearchProduct> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (OtherResearchProduct) r)
                 .map(o -> new ObjectMapper().writeValueAsString(o))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-
-
-    private static JavaRDD<Result> getUpdateForResultDataset(JavaRDD<Row> toupdateresult, JavaPairRDD<String, Result> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
-        return result.leftOuterJoin(toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
-                .map(c -> {
+    private static JavaRDD<Result> getUpdateForResultDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaPairRDD<String, Result> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
+        return result.leftOuterJoin(
+                        toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
+                .map(
+                        c -> {
                             if (!c._2()._2().isPresent()) {
                                 return c._2()._1();
                             }
@@ -315,13 +464,21 @@ public class SparkResultToCommunityThroughSemRelJob {
                                 }
                             }
 
-                    List<Context> contextList = context_set.stream().map(co -> {
+                            List<Context> contextList =
+                                    context_set.stream()
+                                            .map(
+                                                    co -> {
                                                         Context newContext = new Context();
                                                         newContext.setId(co);
-                        newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+                                                        newContext.setDataInfo(
+                                                                Arrays.asList(
+                                                                        getDataInfo(
+                                                                                PROPAGATION_DATA_INFO_TYPE,
+                                                                                class_id,
+                                                                                class_name)));
                                                         return newContext;
-
-                    }).collect(Collectors.toList());
+                                                    })
+                                            .collect(Collectors.toList());
 
                             if (contextList.size() > 0) {
                                 Result r = new Result();
@@ -330,8 +487,8 @@ public class SparkResultToCommunityThroughSemRelJob {
                                 return r;
                             }
                             return null;
-                }).filter(r -> r != null);
-
+                        })
+                .filter(r -> r != null);
 
         //        return toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
         //                .join(result)
@@ -353,7 +510,9 @@ public class SparkResultToCommunityThroughSemRelJob {
         //                    List<Context> contextList = context_set.stream().map(co -> {
         //                        Context newContext = new Context();
         //                        newContext.setId(co);
-//                        newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+        //
+        // newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id,
+        // class_name)));
         //                       return newContext;
         //
         //                    }).collect(Collectors.toList());
@@ -369,11 +528,16 @@ public class SparkResultToCommunityThroughSemRelJob {
         //                .filter(r -> r != null);
     }
 
-    private static JavaRDD<Software> createUpdateForSoftwareDataset(JavaRDD<Row> toupdateresult, List<String> communityList,
-                                                                    JavaRDD<Software> result, String class_id, String class_name) {
-        return result
-                .mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
-                .map(c -> {
+    private static JavaRDD<Software> createUpdateForSoftwareDataset(
+            JavaRDD<Row> toupdateresult,
+            List<String> communityList,
+            JavaRDD<Software> result,
+            String class_id,
+            String class_name) {
+        return result.mapToPair(s -> new Tuple2<>(s.getId(), s))
+                .leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
+                .map(
+                        c -> {
                             Software oaf = c._2()._1();
                             if (c._2()._2().isPresent()) {
 
@@ -381,10 +545,18 @@ public class SparkResultToCommunityThroughSemRelJob {
 
                                 for (Context context : oaf.getContext()) {
                                     if (contexts.contains(context.getId())) {
-                                if (!context.getDataInfo().stream().map(di -> di.getInferenceprovenance())
-                                        .collect(Collectors.toSet()).contains(PROPAGATION_DATA_INFO_TYPE)){
-                                    context.getDataInfo().add(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name));
-                                    //community id already in the context of the result. Remove it from the set that has to be added
+                                        if (!context.getDataInfo().stream()
+                                                .map(di -> di.getInferenceprovenance())
+                                                .collect(Collectors.toSet())
+                                                .contains(PROPAGATION_DATA_INFO_TYPE)) {
+                                            context.getDataInfo()
+                                                    .add(
+                                                            getDataInfo(
+                                                                    PROPAGATION_DATA_INFO_TYPE,
+                                                                    class_id,
+                                                                    class_name));
+                                            // community id already in the context of the result.
+                                            // Remove it from the set that has to be added
                                             contexts.remove(context.getId());
                                         }
                                     }
@@ -393,19 +565,24 @@ public class SparkResultToCommunityThroughSemRelJob {
                                 for (String cId : contexts) {
                                     Context context = new Context();
                                     context.setId(cId);
-                            context.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+                                    context.setDataInfo(
+                                            Arrays.asList(
+                                                    getDataInfo(
+                                                            PROPAGATION_DATA_INFO_TYPE,
+                                                            class_id,
+                                                            class_name)));
                                     cc.add(context);
                                 }
                                 oaf.setContext(cc);
-
                             }
                             return oaf;
                         });
     }
 
-    private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(JavaRDD<Row> toupdateresult, List<String> communityList) {
-        return toupdateresult.mapToPair(c -> {
-
+    private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(
+            JavaRDD<Row> toupdateresult, List<String> communityList) {
+        return toupdateresult.mapToPair(
+                c -> {
                     List<String> contextList = new ArrayList<>();
                     List<String> contexts = c.getList(1);
                     for (String context : contexts) {
@@ -418,21 +595,22 @@ public class SparkResultToCommunityThroughSemRelJob {
                 });
     }
 
-
     private static org.apache.spark.sql.Dataset<Row> getContext(SparkSession spark, String table) {
-        String query = "SELECT relation.source, " + table +".context , relation.target " +
-                "FROM " + table  +
-                " JOIN relation  " +
-                "ON  id = source" ;
+        String query =
+                "SELECT relation.source, "
+                        + table
+                        + ".context , relation.target "
+                        + "FROM "
+                        + table
+                        + " JOIN relation  "
+                        + "ON  id = source";
 
         return spark.sql(query);
     }
 
     private static Boolean relatedToCommunities(Result r, List<String> communityIdList) {
-        Set<String> result_communities = r.getContext()
-                .stream()
-                .map(c -> c.getId())
-                .collect(Collectors.toSet());
+        Set<String> result_communities =
+                r.getContext().stream().map(c -> c.getId()).collect(Collectors.toSet());
         for (String communityId : result_communities) {
             if (communityIdList.contains(communityId)) {
                 return true;
@@ -441,18 +619,33 @@ public class SparkResultToCommunityThroughSemRelJob {
         return false;
     }
 
-    private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
+    private static void updateResult(
+            JavaPairRDD<String, Result> results,
+            JavaPairRDD<String, TypedRow> toupdateresult,
+            String outputPath,
+            String type) {
         results.leftOuterJoin(toupdateresult)
-                .map(p -> {
+                .map(
+                        p -> {
                             Result r = p._2()._1();
                             if (p._2()._2().isPresent()) {
                                 Set<String> communityList = p._2()._2().get().getAccumulator();
                                 for (Context c : r.getContext()) {
                                     if (communityList.contains(c.getId())) {
-                                //verify if the datainfo for this context contains propagation
-                                if (!c.getDataInfo().stream().map(di -> di.getInferenceprovenance()).collect(Collectors.toSet()).contains(PROPAGATION_DATA_INFO_TYPE)){
-                                    c.getDataInfo().add(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
-                                    //community id already in the context of the result. Remove it from the set that has to be added
+                                        // verify if the datainfo for this context contains
+                                        // propagation
+                                        if (!c.getDataInfo().stream()
+                                                .map(di -> di.getInferenceprovenance())
+                                                .collect(Collectors.toSet())
+                                                .contains(PROPAGATION_DATA_INFO_TYPE)) {
+                                            c.getDataInfo()
+                                                    .add(
+                                                            getDataInfo(
+                                                                    PROPAGATION_DATA_INFO_TYPE,
+                                                                    PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                                                                    PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
+                                            // community id already in the context of the result.
+                                            // Remove it from the set that has to be added
                                             communityList.remove(c.getId());
                                         }
                                     }
@@ -461,7 +654,12 @@ public class SparkResultToCommunityThroughSemRelJob {
                                 for (String cId : communityList) {
                                     Context context = new Context();
                                     context.setId(cId);
-                            context.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
+                                    context.setDataInfo(
+                                            Arrays.asList(
+                                                    getDataInfo(
+                                                            PROPAGATION_DATA_INFO_TYPE,
+                                                            PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                                                            PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
                                     cc.add(context);
                                 }
                                 r.setContext(cc);
@@ -472,13 +670,10 @@ public class SparkResultToCommunityThroughSemRelJob {
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-
-
-    private static TypedRow getTypedRow(List<String> communityIdList, List<Context> context, String id, String type) {
-        Set<String> result_communities = context
-                .stream()
-                .map(c -> c.getId())
-                .collect(Collectors.toSet());
+    private static TypedRow getTypedRow(
+            List<String> communityIdList, List<Context> context, String id, String type) {
+        Set<String> result_communities =
+                context.stream().map(c -> c.getId()).collect(Collectors.toSet());
         TypedRow tp = new TypedRow();
         tp.setSourceId(id);
         tp.setType(type);

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob2.java

@@ -1,10 +1,14 @@
 package eu.dnetlib.dhp.resulttocommunityfromsemrel;
 
+import static eu.dnetlib.dhp.PropagationConstant.*;
+
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.QueryInformationSystem;
 import eu.dnetlib.dhp.TypedRow;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.*;
+import java.util.*;
+import java.util.stream.Collectors;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.spark.SparkConf;
@@ -16,23 +20,20 @@ import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import scala.Tuple2;
 
-import java.util.*;
-import java.util.stream.Collectors;
-
-import static eu.dnetlib.dhp.PropagationConstant.*;
-
 public class SparkResultToCommunityThroughSemRelJob2 {
     public static void main(String[] args) throws Exception {
 
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils
-                .toString(SparkResultToCommunityThroughSemRelJob2.class
-                        .getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_propagationresultcommunityfromsemrel_parameters.json")));
+        final ArgumentApplicationParser parser =
+                new ArgumentApplicationParser(
+                        IOUtils.toString(
+                                SparkResultToCommunityThroughSemRelJob2.class.getResourceAsStream(
+                                        "/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")));
         parser.parseArgument(args);
 
         SparkConf conf = new SparkConf();
         conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
-        final SparkSession spark = SparkSession
-                .builder()
+        final SparkSession spark =
+                SparkSession.builder()
                         .appName(SparkResultToCommunityThroughSemRelJob2.class.getSimpleName())
                         .master(parser.get("master"))
                         .config(conf)
@@ -45,50 +46,59 @@ public class SparkResultToCommunityThroughSemRelJob2 {
 
         final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
         // final List<String> allowedsemrel = Arrays.asList("isSupplementedBy", "isSupplementTo");
-        final List<String> communityIdList = QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
-        //final List<String> communityIdList = QueryInformationSystem.getCommunityList("http://beta.services.openaire.eu:8280/is/services/isLookUp");
+        final List<String> communityIdList =
+                QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
+        // final List<String> communityIdList =
+        // QueryInformationSystem.getCommunityList("http://beta.services.openaire.eu:8280/is/services/isLookUp");
 
         createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
 
-
-        JavaRDD<Publication> publication_rdd = sc.textFile(inputPath + "/publication")
+        JavaRDD<Publication> publication_rdd =
+                sc.textFile(inputPath + "/publication")
                         .map(item -> new ObjectMapper().readValue(item, Publication.class));
 
         System.out.println(publication_rdd.count());
         //        JavaRDD<Dataset> dataset_rdd = sc.textFile(inputPath + "/dataset")
         //                .map(item -> new ObjectMapper().readValue(item, Dataset.class));
         //
-//        JavaRDD<OtherResearchProduct> orp_rdd = sc.textFile(inputPath + "/otherresearchproduct")
-//                .map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class));
+        //        JavaRDD<OtherResearchProduct> orp_rdd = sc.textFile(inputPath +
+        // "/otherresearchproduct")
+        //                .map(item -> new ObjectMapper().readValue(item,
+        // OtherResearchProduct.class));
         //
         //        JavaRDD<Software> software_rdd = sc.textFile(inputPath + "/software")
         //                .map(item -> new ObjectMapper().readValue(item, Software.class));
 
-        JavaRDD<Relation> relation_rdd = sc.textFile(inputPath + "/relation")
+        JavaRDD<Relation> relation_rdd =
+                sc.textFile(inputPath + "/relation")
                         .map(item -> new ObjectMapper().readValue(item, Relation.class));
 
         System.out.println(relation_rdd.count());
 
         //                .filter(r -> !r.getDataInfo().getDeletedbyinference())
-//                .filter(r -> allowedsemrel.contains(r.getRelClass()) && RELATION_RESULTRESULT_REL_TYPE.equals(r.getRelType())).cache();
+        //                .filter(r -> allowedsemrel.contains(r.getRelClass()) &&
+        // RELATION_RESULTRESULT_REL_TYPE.equals(r.getRelType())).cache();
 
+        org.apache.spark.sql.Dataset<Publication> publication =
+                spark.createDataset(publication_rdd.rdd(), Encoders.bean(Publication.class));
 
-        org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(publication_rdd.rdd(),
-                Encoders.bean(Publication.class));
+        org.apache.spark.sql.Dataset<Relation> relation =
+                spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
 
-        org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(relation_rdd.rdd(),
-                Encoders.bean(Relation.class));
-
-//        org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(dataset_rdd.rdd(),
+        //        org.apache.spark.sql.Dataset<Dataset> dataset =
+        // spark.createDataset(dataset_rdd.rdd(),
         //                Encoders.bean(Dataset.class));
         //
-//        org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(orp_rdd.rdd(),
+        //        org.apache.spark.sql.Dataset<OtherResearchProduct> other =
+        // spark.createDataset(orp_rdd.rdd(),
         //                Encoders.bean(OtherResearchProduct.class));
         //
-//        org.apache.spark.sql.Dataset<Software> software = spark.createDataset(software_rdd.rdd(),
+        //        org.apache.spark.sql.Dataset<Software> software =
+        // spark.createDataset(software_rdd.rdd(),
         //                Encoders.bean(Software.class));
         //
-//        org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(relation_rdd.rdd(),
+        //        org.apache.spark.sql.Dataset<Relation> relation =
+        // spark.createDataset(relation_rdd.rdd(),
         //                Encoders.bean(Relation.class));
 
         publication.createOrReplaceTempView("publication");
@@ -102,39 +112,40 @@ public class SparkResultToCommunityThroughSemRelJob2 {
 
         String semrellist = getConstraintList(" relClass = '", allowedsemrel);
 
-
-        String query = "Select source, community_context, target " +
-                "from (select id, collect_set(co.id) community_context " +
-                "from  publication " +
-                "lateral view explode (context) c as co " +
-                "where datainfo.deletedbyinference = false "+ communitylist +
-                " group by id) p " +
-                "JOIN " +
-                "(select * " +
-                "from relation " +
-                "where datainfo.deletedbyinference = false and (relClass = 'isSupplementedBy' OR relClass = 'isSupplementTo')) r " +
-                "ON p.id = r.source";
-
+        String query =
+                "Select source, community_context, target "
+                        + "from (select id, collect_set(co.id) community_context "
+                        + "from  publication "
+                        + "lateral view explode (context) c as co "
+                        + "where datainfo.deletedbyinference = false "
+                        + communitylist
+                        + " group by id) p "
+                        + "JOIN "
+                        + "(select * "
+                        + "from relation "
+                        + "where datainfo.deletedbyinference = false and (relClass = 'isSupplementedBy' OR relClass = 'isSupplementTo')) r "
+                        + "ON p.id = r.source";
 
         org.apache.spark.sql.Dataset<Row> publication_context = spark.sql(query);
         publication_context.createOrReplaceTempView("publication_context");
 
         // ( source, (mes, dh-ch-, ni), target )
-        query = "select target , collect_set(co) " +
-                "from (select target, community_context " +
-                "from publication_context pc join publication p on " +
-                "p.id = pc.source) tmp " +
-                "lateral view explode (community_context) c as co " +
-                "group by target";
-
-
+        query =
+                "select target , collect_set(co) "
+                        + "from (select target, community_context "
+                        + "from publication_context pc join publication p on "
+                        + "p.id = pc.source) tmp "
+                        + "lateral view explode (community_context) c as co "
+                        + "group by target";
 
         org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult = spark.sql(query);
 
         System.out.println(toupdatepublicationreresult.count());
 
-        toupdatepublicationreresult.toJavaRDD()
-                .map(r -> {
+        toupdatepublicationreresult
+                .toJavaRDD()
+                .map(
+                        r -> {
                             TypedRow tp = new TypedRow();
                             tp.setSourceId(r.getString(0));
                             r.getList(1).stream().forEach(c -> tp.add((String) c));
@@ -164,35 +175,55 @@ public class SparkResultToCommunityThroughSemRelJob2 {
         //                .saveAsTextFile(outputPath + "/community2semrel");
         //
 
-//        org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult = getUpdateCommunitiesForTable(spark, "software");
-//        org.apache.spark.sql.Dataset<Row> toupdatedatasetresult = getUpdateCommunitiesForTable(spark, "dataset");
-//        org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult = getUpdateCommunitiesForTable(spark, "publication");
-//        org.apache.spark.sql.Dataset<Row> toupdateotherresult = getUpdateCommunitiesForTable(spark, "other");
+        //        org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult =
+        // getUpdateCommunitiesForTable(spark, "software");
+        //        org.apache.spark.sql.Dataset<Row> toupdatedatasetresult =
+        // getUpdateCommunitiesForTable(spark, "dataset");
+        //        org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult =
+        // getUpdateCommunitiesForTable(spark, "publication");
+        //        org.apache.spark.sql.Dataset<Row> toupdateotherresult =
+        // getUpdateCommunitiesForTable(spark, "other");
 
-//        createUpdateForResultDatasetWrite(toupdatesoftwareresult.toJavaRDD(), outputPath, "software_update",
-//                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        //        createUpdateForResultDatasetWrite(toupdatesoftwareresult.toJavaRDD(), outputPath,
+        // "software_update",
+        //                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+        // PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
         //
-//        createUpdateForResultDatasetWrite(toupdatedatasetresult.toJavaRDD(),  outputPath, "dataset_update",
-//                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        //        createUpdateForResultDatasetWrite(toupdatedatasetresult.toJavaRDD(),  outputPath,
+        // "dataset_update",
+        //                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+        // PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
 
-//        createUpdateForResultDatasetWrite(toupdatepublicationreresult.toJavaRDD(),  outputPath, "publication_update",
-//                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        //        createUpdateForResultDatasetWrite(toupdatepublicationreresult.toJavaRDD(),
+        // outputPath, "publication_update",
+        //                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+        // PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
 
-//        createUpdateForResultDatasetWrite(toupdateotherresult.toJavaRDD(), outputPath, "other_update",
-//                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        //        createUpdateForResultDatasetWrite(toupdateotherresult.toJavaRDD(), outputPath,
+        // "other_update",
+        //                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+        // PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
         //
         //
-//        updateForDatasetDataset(toupdatedatasetresult.toJavaRDD(), dataset.toJavaRDD(), outputPath, "dataset",
-//                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        //        updateForDatasetDataset(toupdatedatasetresult.toJavaRDD(), dataset.toJavaRDD(),
+        // outputPath, "dataset",
+        //                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+        // PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
         //
-//        updateForOtherDataset(toupdateotherresult.toJavaRDD(), other.toJavaRDD(), outputPath, "otherresearchproduct",
-//                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        //        updateForOtherDataset(toupdateotherresult.toJavaRDD(), other.toJavaRDD(),
+        // outputPath, "otherresearchproduct",
+        //                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+        // PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
         //
-//        updateForSoftwareDataset(toupdatesoftwareresult.toJavaRDD(), software.toJavaRDD(), outputPath, "software",
-//                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        //        updateForSoftwareDataset(toupdatesoftwareresult.toJavaRDD(), software.toJavaRDD(),
+        // outputPath, "software",
+        //                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+        // PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
         //
-//        updateForPublicationDataset(toupdatepublicationreresult.toJavaRDD(), publication.toJavaRDD(), outputPath, "publication",
-//                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        //        updateForPublicationDataset(toupdatepublicationreresult.toJavaRDD(),
+        // publication.toJavaRDD(), outputPath, "publication",
+        //                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+        // PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
         //
 
         /*
@@ -233,45 +264,67 @@ public class SparkResultToCommunityThroughSemRelJob2 {
         */
     }
 
-   private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(SparkSession spark, String table){
-        String query = "SELECT target_id, collect_set(co.id) context_id  " +
-                "       FROM (SELECT t.id target_id, s.context source_context " +
-                "             FROM context_software s " +
-                "             JOIN " + table + " t " +
-                "             ON s.target = t.id " +
-                "             UNION ALL " +
-                "             SELECT t.id target_id, d.context source_context " +
-                "             FROM dataset_context d  " +
-                "             JOIN " + table + " t" +
-                "             ON s.target = t.id  " +
-                "             UNION ALL  " +
-                "             SELECT t.id target_id, p.context source_context " +
-                "             FROM publication_context p" +
-                "             JOIN " + table +" t " +
-                "             on p.target = t.id " +
-                "             UNION ALL " +
-                "             SELECT t.id target_id, o.context source_context " +
-                "             FROM other_context o " +
-                "             JOIN " + table + " t  " +
-                "             ON o.target = t.id)  TMP " +
-                "             LATERAL VIEW EXPLODE(source_context) MyT as co " +
-                "             GROUP BY target_id" ;
+    private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(
+            SparkSession spark, String table) {
+        String query =
+                "SELECT target_id, collect_set(co.id) context_id  "
+                        + "       FROM (SELECT t.id target_id, s.context source_context "
+                        + "             FROM context_software s "
+                        + "             JOIN "
+                        + table
+                        + " t "
+                        + "             ON s.target = t.id "
+                        + "             UNION ALL "
+                        + "             SELECT t.id target_id, d.context source_context "
+                        + "             FROM dataset_context d  "
+                        + "             JOIN "
+                        + table
+                        + " t"
+                        + "             ON s.target = t.id  "
+                        + "             UNION ALL  "
+                        + "             SELECT t.id target_id, p.context source_context "
+                        + "             FROM publication_context p"
+                        + "             JOIN "
+                        + table
+                        + " t "
+                        + "             on p.target = t.id "
+                        + "             UNION ALL "
+                        + "             SELECT t.id target_id, o.context source_context "
+                        + "             FROM other_context o "
+                        + "             JOIN "
+                        + table
+                        + " t  "
+                        + "             ON o.target = t.id)  TMP "
+                        + "             LATERAL VIEW EXPLODE(source_context) MyT as co "
+                        + "             GROUP BY target_id";
 
         return spark.sql(query);
     }
 
-    private static JavaRDD<Result> createUpdateForResultDatasetWrite(JavaRDD<Row> toupdateresult, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
-        return toupdateresult.map(r -> {
+    private static JavaRDD<Result> createUpdateForResultDatasetWrite(
+            JavaRDD<Row> toupdateresult,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
+        return toupdateresult
+                .map(
+                        r -> {
                             List<Context> contextList = new ArrayList();
                             List<String> toAddContext = r.getList(1);
                             for (String cId : toAddContext) {
                                 if (communityIdList.contains(cId)) {
                                     Context newContext = new Context();
                                     newContext.setId(cId);
-                    newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+                                    newContext.setDataInfo(
+                                            Arrays.asList(
+                                                    getDataInfo(
+                                                            PROPAGATION_DATA_INFO_TYPE,
+                                                            class_id,
+                                                            class_name)));
                                     contextList.add(newContext);
                                 }
-
                             }
 
                             if (contextList.size() > 0) {
@@ -281,46 +334,110 @@ public class SparkResultToCommunityThroughSemRelJob2 {
                                 return ret;
                             }
                             return null;
-        }).filter(r -> r != null);
+                        })
+                .filter(r -> r != null);
     }
 
-    private static void updateForSoftwareDataset(JavaRDD<Row> toupdateresult, JavaRDD<Software> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForSoftwareDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<Software> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (Software) r)
                 .map(s -> new ObjectMapper().writeValueAsString(s))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-    private static void updateForDatasetDataset(JavaRDD<Row> toupdateresult, JavaRDD<Dataset> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForDatasetDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<Dataset> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (Dataset) r)
                 .map(d -> new ObjectMapper().writeValueAsString(d))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-    private static void updateForPublicationDataset(JavaRDD<Row> toupdateresult, JavaRDD<Publication> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForPublicationDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<Publication> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (Publication) r)
                 .map(p -> new ObjectMapper().writeValueAsString(p))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-    private static void updateForOtherDataset(JavaRDD<Row> toupdateresult, JavaRDD<OtherResearchProduct> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForOtherDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<OtherResearchProduct> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (OtherResearchProduct) r)
                 .map(o -> new ObjectMapper().writeValueAsString(o))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-
-
-    private static JavaRDD<Result> getUpdateForResultDataset(JavaRDD<Row> toupdateresult, JavaPairRDD<String, Result> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
-        return result.leftOuterJoin(toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
-                .map(c -> {
+    private static JavaRDD<Result> getUpdateForResultDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaPairRDD<String, Result> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
+        return result.leftOuterJoin(
+                        toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
+                .map(
+                        c -> {
                             if (!c._2()._2().isPresent()) {
                                 return c._2()._1();
                             }
@@ -339,13 +456,21 @@ public class SparkResultToCommunityThroughSemRelJob2 {
                                 }
                             }
 
-                    List<Context> contextList = context_set.stream().map(co -> {
+                            List<Context> contextList =
+                                    context_set.stream()
+                                            .map(
+                                                    co -> {
                                                         Context newContext = new Context();
                                                         newContext.setId(co);
-                        newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+                                                        newContext.setDataInfo(
+                                                                Arrays.asList(
+                                                                        getDataInfo(
+                                                                                PROPAGATION_DATA_INFO_TYPE,
+                                                                                class_id,
+                                                                                class_name)));
                                                         return newContext;
-
-                    }).collect(Collectors.toList());
+                                                    })
+                                            .collect(Collectors.toList());
 
                             if (contextList.size() > 0) {
                                 Result r = new Result();
@@ -354,8 +479,8 @@ public class SparkResultToCommunityThroughSemRelJob2 {
                                 return r;
                             }
                             return null;
-                }).filter(r -> r != null);
-
+                        })
+                .filter(r -> r != null);
 
         //        return toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
         //                .join(result)
@@ -377,7 +502,9 @@ public class SparkResultToCommunityThroughSemRelJob2 {
         //                    List<Context> contextList = context_set.stream().map(co -> {
         //                        Context newContext = new Context();
         //                        newContext.setId(co);
-//                        newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+        //
+        // newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id,
+        // class_name)));
         //                       return newContext;
         //
         //                    }).collect(Collectors.toList());
@@ -393,11 +520,16 @@ public class SparkResultToCommunityThroughSemRelJob2 {
         //                .filter(r -> r != null);
     }
 
-    private static JavaRDD<Software> createUpdateForSoftwareDataset(JavaRDD<Row> toupdateresult, List<String> communityList,
-                                                                    JavaRDD<Software> result, String class_id, String class_name) {
-        return result
-                .mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
-                .map(c -> {
+    private static JavaRDD<Software> createUpdateForSoftwareDataset(
+            JavaRDD<Row> toupdateresult,
+            List<String> communityList,
+            JavaRDD<Software> result,
+            String class_id,
+            String class_name) {
+        return result.mapToPair(s -> new Tuple2<>(s.getId(), s))
+                .leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
+                .map(
+                        c -> {
                             Software oaf = c._2()._1();
                             if (c._2()._2().isPresent()) {
 
@@ -405,10 +537,18 @@ public class SparkResultToCommunityThroughSemRelJob2 {
 
                                 for (Context context : oaf.getContext()) {
                                     if (contexts.contains(context.getId())) {
-                                if (!context.getDataInfo().stream().map(di -> di.getInferenceprovenance())
-                                        .collect(Collectors.toSet()).contains(PROPAGATION_DATA_INFO_TYPE)){
-                                    context.getDataInfo().add(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name));
-                                    //community id already in the context of the result. Remove it from the set that has to be added
+                                        if (!context.getDataInfo().stream()
+                                                .map(di -> di.getInferenceprovenance())
+                                                .collect(Collectors.toSet())
+                                                .contains(PROPAGATION_DATA_INFO_TYPE)) {
+                                            context.getDataInfo()
+                                                    .add(
+                                                            getDataInfo(
+                                                                    PROPAGATION_DATA_INFO_TYPE,
+                                                                    class_id,
+                                                                    class_name));
+                                            // community id already in the context of the result.
+                                            // Remove it from the set that has to be added
                                             contexts.remove(context.getId());
                                         }
                                     }
@@ -417,19 +557,24 @@ public class SparkResultToCommunityThroughSemRelJob2 {
                                 for (String cId : contexts) {
                                     Context context = new Context();
                                     context.setId(cId);
-                            context.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+                                    context.setDataInfo(
+                                            Arrays.asList(
+                                                    getDataInfo(
+                                                            PROPAGATION_DATA_INFO_TYPE,
+                                                            class_id,
+                                                            class_name)));
                                     cc.add(context);
                                 }
                                 oaf.setContext(cc);
-
                             }
                             return oaf;
                         });
     }
 
-    private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(JavaRDD<Row> toupdateresult, List<String> communityList) {
-        return toupdateresult.mapToPair(c -> {
-
+    private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(
+            JavaRDD<Row> toupdateresult, List<String> communityList) {
+        return toupdateresult.mapToPair(
+                c -> {
                     List<String> contextList = new ArrayList<>();
                     List<String> contexts = c.getList(1);
                     for (String context : contexts) {
@@ -442,21 +587,22 @@ public class SparkResultToCommunityThroughSemRelJob2 {
                 });
     }
 
-
     private static org.apache.spark.sql.Dataset<Row> getContext(SparkSession spark, String table) {
-        String query = "SELECT relation.source, " + table +".context , relation.target " +
-                "FROM " + table  +
-                " JOIN relation  " +
-                "ON  id = source" ;
+        String query =
+                "SELECT relation.source, "
+                        + table
+                        + ".context , relation.target "
+                        + "FROM "
+                        + table
+                        + " JOIN relation  "
+                        + "ON  id = source";
 
         return spark.sql(query);
     }
 
     private static Boolean relatedToCommunities(Result r, List<String> communityIdList) {
-        Set<String> result_communities = r.getContext()
-                .stream()
-                .map(c -> c.getId())
-                .collect(Collectors.toSet());
+        Set<String> result_communities =
+                r.getContext().stream().map(c -> c.getId()).collect(Collectors.toSet());
         for (String communityId : result_communities) {
             if (communityIdList.contains(communityId)) {
                 return true;
@@ -465,18 +611,33 @@ public class SparkResultToCommunityThroughSemRelJob2 {
         return false;
     }
 
-    private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
+    private static void updateResult(
+            JavaPairRDD<String, Result> results,
+            JavaPairRDD<String, TypedRow> toupdateresult,
+            String outputPath,
+            String type) {
         results.leftOuterJoin(toupdateresult)
-                .map(p -> {
+                .map(
+                        p -> {
                             Result r = p._2()._1();
                             if (p._2()._2().isPresent()) {
                                 Set<String> communityList = p._2()._2().get().getAccumulator();
                                 for (Context c : r.getContext()) {
                                     if (communityList.contains(c.getId())) {
-                                //verify if the datainfo for this context contains propagation
-                                if (!c.getDataInfo().stream().map(di -> di.getInferenceprovenance()).collect(Collectors.toSet()).contains(PROPAGATION_DATA_INFO_TYPE)){
-                                    c.getDataInfo().add(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
-                                    //community id already in the context of the result. Remove it from the set that has to be added
+                                        // verify if the datainfo for this context contains
+                                        // propagation
+                                        if (!c.getDataInfo().stream()
+                                                .map(di -> di.getInferenceprovenance())
+                                                .collect(Collectors.toSet())
+                                                .contains(PROPAGATION_DATA_INFO_TYPE)) {
+                                            c.getDataInfo()
+                                                    .add(
+                                                            getDataInfo(
+                                                                    PROPAGATION_DATA_INFO_TYPE,
+                                                                    PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                                                                    PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
+                                            // community id already in the context of the result.
+                                            // Remove it from the set that has to be added
                                             communityList.remove(c.getId());
                                         }
                                     }
@@ -485,7 +646,12 @@ public class SparkResultToCommunityThroughSemRelJob2 {
                                 for (String cId : communityList) {
                                     Context context = new Context();
                                     context.setId(cId);
-                            context.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
+                                    context.setDataInfo(
+                                            Arrays.asList(
+                                                    getDataInfo(
+                                                            PROPAGATION_DATA_INFO_TYPE,
+                                                            PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                                                            PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
                                     cc.add(context);
                                 }
                                 r.setContext(cc);
@@ -496,13 +662,10 @@ public class SparkResultToCommunityThroughSemRelJob2 {
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-
-
-    private static TypedRow getTypedRow(List<String> communityIdList, List<Context> context, String id, String type) {
-        Set<String> result_communities = context
-                .stream()
-                .map(c -> c.getId())
-                .collect(Collectors.toSet());
+    private static TypedRow getTypedRow(
+            List<String> communityIdList, List<Context> context, String id, String type) {
+        Set<String> result_communities =
+                context.stream().map(c -> c.getId()).collect(Collectors.toSet());
         TypedRow tp = new TypedRow();
         tp.setSourceId(id);
         tp.setType(type);

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob3.java

@@ -1,10 +1,14 @@
 package eu.dnetlib.dhp.resulttocommunityfromsemrel;
 
+import static eu.dnetlib.dhp.PropagationConstant.*;
+
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.QueryInformationSystem;
 import eu.dnetlib.dhp.TypedRow;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.*;
+import java.util.*;
+import java.util.stream.Collectors;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.spark.SparkConf;
@@ -16,23 +20,20 @@ import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import scala.Tuple2;
 
-import java.util.*;
-import java.util.stream.Collectors;
-
-import static eu.dnetlib.dhp.PropagationConstant.*;
-
 public class SparkResultToCommunityThroughSemRelJob3 {
     public static void main(String[] args) throws Exception {
 
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils
-                .toString(SparkResultToCommunityThroughSemRelJob3.class
-                        .getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_propagationresultcommunityfromsemrel_parameters.json")));
+        final ArgumentApplicationParser parser =
+                new ArgumentApplicationParser(
+                        IOUtils.toString(
+                                SparkResultToCommunityThroughSemRelJob3.class.getResourceAsStream(
+                                        "/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json")));
         parser.parseArgument(args);
 
         SparkConf conf = new SparkConf();
         conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
-        final SparkSession spark = SparkSession
-                .builder()
+        final SparkSession spark =
+                SparkSession.builder()
                         .appName(SparkResultToCommunityThroughSemRelJob3.class.getSimpleName())
                         .master(parser.get("master"))
                         .config(conf)
@@ -45,42 +46,48 @@ public class SparkResultToCommunityThroughSemRelJob3 {
 
         final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
 
-        final List<String> communityIdList = QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
+        final List<String> communityIdList =
+                QueryInformationSystem.getCommunityList(parser.get("isLookupUrl"));
 
         createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
 
-
-        JavaRDD<Publication> publication_rdd = sc.textFile(inputPath + "/publication")
+        JavaRDD<Publication> publication_rdd =
+                sc.textFile(inputPath + "/publication")
                         .map(item -> new ObjectMapper().readValue(item, Publication.class));
 
-        JavaRDD<Dataset> dataset_rdd = sc.textFile(inputPath + "/dataset")
+        JavaRDD<Dataset> dataset_rdd =
+                sc.textFile(inputPath + "/dataset")
                         .map(item -> new ObjectMapper().readValue(item, Dataset.class));
 
-        JavaRDD<OtherResearchProduct> orp_rdd = sc.textFile(inputPath + "/otherresearchproduct")
-                .map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class));
+        JavaRDD<OtherResearchProduct> orp_rdd =
+                sc.textFile(inputPath + "/otherresearchproduct")
+                        .map(
+                                item ->
+                                        new ObjectMapper()
+                                                .readValue(item, OtherResearchProduct.class));
 
-        JavaRDD<Software> software_rdd = sc.textFile(inputPath + "/software")
+        JavaRDD<Software> software_rdd =
+                sc.textFile(inputPath + "/software")
                         .map(item -> new ObjectMapper().readValue(item, Software.class));
 
-        JavaRDD<Relation> relation_rdd = sc.textFile(inputPath + "/relation")
+        JavaRDD<Relation> relation_rdd =
+                sc.textFile(inputPath + "/relation")
                         .map(item -> new ObjectMapper().readValue(item, Relation.class));
 
+        org.apache.spark.sql.Dataset<Publication> publication =
+                spark.createDataset(publication_rdd.rdd(), Encoders.bean(Publication.class));
 
-        org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(publication_rdd.rdd(),
-                Encoders.bean(Publication.class));
+        org.apache.spark.sql.Dataset<Relation> relation =
+                spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
 
-        org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(relation_rdd.rdd(),
-                Encoders.bean(Relation.class));
+        org.apache.spark.sql.Dataset<Dataset> dataset =
+                spark.createDataset(dataset_rdd.rdd(), Encoders.bean(Dataset.class));
 
-        org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(dataset_rdd.rdd(),
-                Encoders.bean(Dataset.class));
-
-        org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(orp_rdd.rdd(),
-                Encoders.bean(OtherResearchProduct.class));
-
-        org.apache.spark.sql.Dataset<Software> software = spark.createDataset(software_rdd.rdd(),
-                Encoders.bean(Software.class));
+        org.apache.spark.sql.Dataset<OtherResearchProduct> other =
+                spark.createDataset(orp_rdd.rdd(), Encoders.bean(OtherResearchProduct.class));
 
+        org.apache.spark.sql.Dataset<Software> software =
+                spark.createDataset(software_rdd.rdd(), Encoders.bean(Software.class));
 
         publication.createOrReplaceTempView("publication");
         relation.createOrReplaceTempView("relation");
@@ -92,61 +99,109 @@ public class SparkResultToCommunityThroughSemRelJob3 {
 
         String semrellist = getConstraintList(" relClass = '", allowedsemrel);
 
-
-        String query = "Select source, community_context, target " +
-                "from (select id, collect_set(co.id) community_context " +
-                "from  publication " +
-                "lateral view explode (context) c as co " +
-                "where datainfo.deletedbyinference = false "+ communitylist +
-                " group by id) p " +
-                "JOIN " +
-                "(select * " +
-                "from relation " +
-                "where datainfo.deletedbyinference = false " + semrellist + ") r " +
-                "ON p.id = r.source";
-
+        String query =
+                "Select source, community_context, target "
+                        + "from (select id, collect_set(co.id) community_context "
+                        + "from  publication "
+                        + "lateral view explode (context) c as co "
+                        + "where datainfo.deletedbyinference = false "
+                        + communitylist
+                        + " group by id) p "
+                        + "JOIN "
+                        + "(select * "
+                        + "from relation "
+                        + "where datainfo.deletedbyinference = false "
+                        + semrellist
+                        + ") r "
+                        + "ON p.id = r.source";
 
         org.apache.spark.sql.Dataset<Row> publication_context = spark.sql(query);
         publication_context.createOrReplaceTempView("publication_context");
 
         // ( source, (mes, dh-ch-, ni), target )
-        query = "select target , collect_set(co) " +
-                "from (select target, community_context " +
-                "from publication_context pc join publication p on " +
-                "p.id = pc.source) tmp " +
-                "lateral view explode (community_context) c as co " +
-                "group by target";
-
-
+        query =
+                "select target , collect_set(co) "
+                        + "from (select target, community_context "
+                        + "from publication_context pc join publication p on "
+                        + "p.id = pc.source) tmp "
+                        + "lateral view explode (community_context) c as co "
+                        + "group by target";
 
         org.apache.spark.sql.Dataset<Row> toupdatepublicationreresult = spark.sql(query);
-        org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult = getUpdateCommunitiesForTable(spark, "software");
-        org.apache.spark.sql.Dataset<Row> toupdatedatasetresult = getUpdateCommunitiesForTable(spark, "dataset");
-        org.apache.spark.sql.Dataset<Row> toupdateotherresult = getUpdateCommunitiesForTable(spark, "other");
+        org.apache.spark.sql.Dataset<Row> toupdatesoftwareresult =
+                getUpdateCommunitiesForTable(spark, "software");
+        org.apache.spark.sql.Dataset<Row> toupdatedatasetresult =
+                getUpdateCommunitiesForTable(spark, "dataset");
+        org.apache.spark.sql.Dataset<Row> toupdateotherresult =
+                getUpdateCommunitiesForTable(spark, "other");
 
-        createUpdateForResultDatasetWrite(toupdatesoftwareresult.toJavaRDD(), outputPath, "software_update",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        createUpdateForResultDatasetWrite(
+                toupdatesoftwareresult.toJavaRDD(),
+                outputPath,
+                "software_update",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        createUpdateForResultDatasetWrite(toupdatedatasetresult.toJavaRDD(),  outputPath, "dataset_update",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        createUpdateForResultDatasetWrite(
+                toupdatedatasetresult.toJavaRDD(),
+                outputPath,
+                "dataset_update",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        createUpdateForResultDatasetWrite(toupdatepublicationreresult.toJavaRDD(),  outputPath, "publication_update",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        createUpdateForResultDatasetWrite(
+                toupdatepublicationreresult.toJavaRDD(),
+                outputPath,
+                "publication_update",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        createUpdateForResultDatasetWrite(toupdateotherresult.toJavaRDD(), outputPath, "other_update",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        createUpdateForResultDatasetWrite(
+                toupdateotherresult.toJavaRDD(),
+                outputPath,
+                "other_update",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        updateForDatasetDataset(toupdatedatasetresult.toJavaRDD(), dataset.toJavaRDD(), outputPath, "dataset",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        updateForDatasetDataset(
+                toupdatedatasetresult.toJavaRDD(),
+                dataset.toJavaRDD(),
+                outputPath,
+                "dataset",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        updateForOtherDataset(toupdateotherresult.toJavaRDD(), other.toJavaRDD(), outputPath, "otherresearchproduct",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        updateForOtherDataset(
+                toupdateotherresult.toJavaRDD(),
+                other.toJavaRDD(),
+                outputPath,
+                "otherresearchproduct",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        updateForSoftwareDataset(toupdatesoftwareresult.toJavaRDD(), software.toJavaRDD(), outputPath, "software",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        updateForSoftwareDataset(
+                toupdatesoftwareresult.toJavaRDD(),
+                software.toJavaRDD(),
+                outputPath,
+                "software",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
 
-        updateForPublicationDataset(toupdatepublicationreresult.toJavaRDD(), publication.toJavaRDD(), outputPath, "publication",
-                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME, communityIdList);
+        updateForPublicationDataset(
+                toupdatepublicationreresult.toJavaRDD(),
+                publication.toJavaRDD(),
+                outputPath,
+                "publication",
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME,
+                communityIdList);
         //
 
         /*
@@ -187,45 +242,67 @@ public class SparkResultToCommunityThroughSemRelJob3 {
         */
     }
 
-   private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(SparkSession spark, String table){
-        String query = "SELECT target_id, collect_set(co.id) context_id  " +
-                "       FROM (SELECT t.id target_id, s.context source_context " +
-                "             FROM context_software s " +
-                "             JOIN " + table + " t " +
-                "             ON s.target = t.id " +
-                "             UNION ALL " +
-                "             SELECT t.id target_id, d.context source_context " +
-                "             FROM dataset_context d  " +
-                "             JOIN " + table + " t" +
-                "             ON s.target = t.id  " +
-                "             UNION ALL  " +
-                "             SELECT t.id target_id, p.context source_context " +
-                "             FROM publication_context p" +
-                "             JOIN " + table +" t " +
-                "             on p.target = t.id " +
-                "             UNION ALL " +
-                "             SELECT t.id target_id, o.context source_context " +
-                "             FROM other_context o " +
-                "             JOIN " + table + " t  " +
-                "             ON o.target = t.id)  TMP " +
-                "             LATERAL VIEW EXPLODE(source_context) MyT as co " +
-                "             GROUP BY target_id" ;
+    private static org.apache.spark.sql.Dataset<Row> getUpdateCommunitiesForTable(
+            SparkSession spark, String table) {
+        String query =
+                "SELECT target_id, collect_set(co.id) context_id  "
+                        + "       FROM (SELECT t.id target_id, s.context source_context "
+                        + "             FROM context_software s "
+                        + "             JOIN "
+                        + table
+                        + " t "
+                        + "             ON s.target = t.id "
+                        + "             UNION ALL "
+                        + "             SELECT t.id target_id, d.context source_context "
+                        + "             FROM dataset_context d  "
+                        + "             JOIN "
+                        + table
+                        + " t"
+                        + "             ON s.target = t.id  "
+                        + "             UNION ALL  "
+                        + "             SELECT t.id target_id, p.context source_context "
+                        + "             FROM publication_context p"
+                        + "             JOIN "
+                        + table
+                        + " t "
+                        + "             on p.target = t.id "
+                        + "             UNION ALL "
+                        + "             SELECT t.id target_id, o.context source_context "
+                        + "             FROM other_context o "
+                        + "             JOIN "
+                        + table
+                        + " t  "
+                        + "             ON o.target = t.id)  TMP "
+                        + "             LATERAL VIEW EXPLODE(source_context) MyT as co "
+                        + "             GROUP BY target_id";
 
         return spark.sql(query);
     }
 
-    private static JavaRDD<Result> createUpdateForResultDatasetWrite(JavaRDD<Row> toupdateresult, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
-        return toupdateresult.map(r -> {
+    private static JavaRDD<Result> createUpdateForResultDatasetWrite(
+            JavaRDD<Row> toupdateresult,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
+        return toupdateresult
+                .map(
+                        r -> {
                             List<Context> contextList = new ArrayList();
                             List<String> toAddContext = r.getList(1);
                             for (String cId : toAddContext) {
                                 if (communityIdList.contains(cId)) {
                                     Context newContext = new Context();
                                     newContext.setId(cId);
-                    newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+                                    newContext.setDataInfo(
+                                            Arrays.asList(
+                                                    getDataInfo(
+                                                            PROPAGATION_DATA_INFO_TYPE,
+                                                            class_id,
+                                                            class_name)));
                                     contextList.add(newContext);
                                 }
-
                             }
 
                             if (contextList.size() > 0) {
@@ -235,46 +312,110 @@ public class SparkResultToCommunityThroughSemRelJob3 {
                                 return ret;
                             }
                             return null;
-        }).filter(r -> r != null);
+                        })
+                .filter(r -> r != null);
     }
 
-    private static void updateForSoftwareDataset(JavaRDD<Row> toupdateresult, JavaRDD<Software> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForSoftwareDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<Software> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (Software) r)
                 .map(s -> new ObjectMapper().writeValueAsString(s))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-    private static void updateForDatasetDataset(JavaRDD<Row> toupdateresult, JavaRDD<Dataset> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForDatasetDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<Dataset> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (Dataset) r)
                 .map(d -> new ObjectMapper().writeValueAsString(d))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-    private static void updateForPublicationDataset(JavaRDD<Row> toupdateresult, JavaRDD<Publication> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForPublicationDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<Publication> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (Publication) r)
                 .map(p -> new ObjectMapper().writeValueAsString(p))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-    private static void updateForOtherDataset(JavaRDD<Row> toupdateresult, JavaRDD<OtherResearchProduct> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
+    private static void updateForOtherDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaRDD<OtherResearchProduct> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
         JavaPairRDD<String, Result> tmp = result.mapToPair(r -> new Tuple2(r.getId(), r));
-        getUpdateForResultDataset(toupdateresult, tmp, outputPath, type, class_id, class_name, communityIdList)
+        getUpdateForResultDataset(
+                        toupdateresult,
+                        tmp,
+                        outputPath,
+                        type,
+                        class_id,
+                        class_name,
+                        communityIdList)
                 .map(r -> (OtherResearchProduct) r)
                 .map(o -> new ObjectMapper().writeValueAsString(o))
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-
-
-    private static JavaRDD<Result> getUpdateForResultDataset(JavaRDD<Row> toupdateresult, JavaPairRDD<String, Result> result, String outputPath, String type, String class_id, String class_name, List<String> communityIdList){
-        return result.leftOuterJoin(toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
-                .map(c -> {
+    private static JavaRDD<Result> getUpdateForResultDataset(
+            JavaRDD<Row> toupdateresult,
+            JavaPairRDD<String, Result> result,
+            String outputPath,
+            String type,
+            String class_id,
+            String class_name,
+            List<String> communityIdList) {
+        return result.leftOuterJoin(
+                        toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))))
+                .map(
+                        c -> {
                             if (!c._2()._2().isPresent()) {
                                 return c._2()._1();
                             }
@@ -293,13 +434,21 @@ public class SparkResultToCommunityThroughSemRelJob3 {
                                 }
                             }
 
-                    List<Context> contextList = context_set.stream().map(co -> {
+                            List<Context> contextList =
+                                    context_set.stream()
+                                            .map(
+                                                    co -> {
                                                         Context newContext = new Context();
                                                         newContext.setId(co);
-                        newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+                                                        newContext.setDataInfo(
+                                                                Arrays.asList(
+                                                                        getDataInfo(
+                                                                                PROPAGATION_DATA_INFO_TYPE,
+                                                                                class_id,
+                                                                                class_name)));
                                                         return newContext;
-
-                    }).collect(Collectors.toList());
+                                                    })
+                                            .collect(Collectors.toList());
 
                             if (contextList.size() > 0) {
                                 Result r = new Result();
@@ -308,8 +457,8 @@ public class SparkResultToCommunityThroughSemRelJob3 {
                                 return r;
                             }
                             return null;
-                }).filter(r -> r != null);
-
+                        })
+                .filter(r -> r != null);
 
         //        return toupdateresult.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
         //                .join(result)
@@ -331,7 +480,9 @@ public class SparkResultToCommunityThroughSemRelJob3 {
         //                    List<Context> contextList = context_set.stream().map(co -> {
         //                        Context newContext = new Context();
         //                        newContext.setId(co);
-//                        newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+        //
+        // newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id,
+        // class_name)));
         //                       return newContext;
         //
         //                    }).collect(Collectors.toList());
@@ -347,11 +498,16 @@ public class SparkResultToCommunityThroughSemRelJob3 {
         //                .filter(r -> r != null);
     }
 
-    private static JavaRDD<Software> createUpdateForSoftwareDataset(JavaRDD<Row> toupdateresult, List<String> communityList,
-                                                                    JavaRDD<Software> result, String class_id, String class_name) {
-        return result
-                .mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
-                .map(c -> {
+    private static JavaRDD<Software> createUpdateForSoftwareDataset(
+            JavaRDD<Row> toupdateresult,
+            List<String> communityList,
+            JavaRDD<Software> result,
+            String class_id,
+            String class_name) {
+        return result.mapToPair(s -> new Tuple2<>(s.getId(), s))
+                .leftOuterJoin(getStringResultJavaPairRDD(toupdateresult, communityList))
+                .map(
+                        c -> {
                             Software oaf = c._2()._1();
                             if (c._2()._2().isPresent()) {
 
@@ -359,10 +515,18 @@ public class SparkResultToCommunityThroughSemRelJob3 {
 
                                 for (Context context : oaf.getContext()) {
                                     if (contexts.contains(context.getId())) {
-                                if (!context.getDataInfo().stream().map(di -> di.getInferenceprovenance())
-                                        .collect(Collectors.toSet()).contains(PROPAGATION_DATA_INFO_TYPE)){
-                                    context.getDataInfo().add(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name));
-                                    //community id already in the context of the result. Remove it from the set that has to be added
+                                        if (!context.getDataInfo().stream()
+                                                .map(di -> di.getInferenceprovenance())
+                                                .collect(Collectors.toSet())
+                                                .contains(PROPAGATION_DATA_INFO_TYPE)) {
+                                            context.getDataInfo()
+                                                    .add(
+                                                            getDataInfo(
+                                                                    PROPAGATION_DATA_INFO_TYPE,
+                                                                    class_id,
+                                                                    class_name));
+                                            // community id already in the context of the result.
+                                            // Remove it from the set that has to be added
                                             contexts.remove(context.getId());
                                         }
                                     }
@@ -371,19 +535,24 @@ public class SparkResultToCommunityThroughSemRelJob3 {
                                 for (String cId : contexts) {
                                     Context context = new Context();
                                     context.setId(cId);
-                            context.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, class_id, class_name)));
+                                    context.setDataInfo(
+                                            Arrays.asList(
+                                                    getDataInfo(
+                                                            PROPAGATION_DATA_INFO_TYPE,
+                                                            class_id,
+                                                            class_name)));
                                     cc.add(context);
                                 }
                                 oaf.setContext(cc);
-
                             }
                             return oaf;
                         });
     }
 
-    private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(JavaRDD<Row> toupdateresult, List<String> communityList) {
-        return toupdateresult.mapToPair(c -> {
-
+    private static JavaPairRDD<String, List<String>> getStringResultJavaPairRDD(
+            JavaRDD<Row> toupdateresult, List<String> communityList) {
+        return toupdateresult.mapToPair(
+                c -> {
                     List<String> contextList = new ArrayList<>();
                     List<String> contexts = c.getList(1);
                     for (String context : contexts) {
@@ -396,21 +565,22 @@ public class SparkResultToCommunityThroughSemRelJob3 {
                 });
     }
 
-
     private static org.apache.spark.sql.Dataset<Row> getContext(SparkSession spark, String table) {
-        String query = "SELECT relation.source, " + table +".context , relation.target " +
-                "FROM " + table  +
-                " JOIN relation  " +
-                "ON  id = source" ;
+        String query =
+                "SELECT relation.source, "
+                        + table
+                        + ".context , relation.target "
+                        + "FROM "
+                        + table
+                        + " JOIN relation  "
+                        + "ON  id = source";
 
         return spark.sql(query);
     }
 
     private static Boolean relatedToCommunities(Result r, List<String> communityIdList) {
-        Set<String> result_communities = r.getContext()
-                .stream()
-                .map(c -> c.getId())
-                .collect(Collectors.toSet());
+        Set<String> result_communities =
+                r.getContext().stream().map(c -> c.getId()).collect(Collectors.toSet());
         for (String communityId : result_communities) {
             if (communityIdList.contains(communityId)) {
                 return true;
@@ -419,18 +589,33 @@ public class SparkResultToCommunityThroughSemRelJob3 {
         return false;
     }
 
-    private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
+    private static void updateResult(
+            JavaPairRDD<String, Result> results,
+            JavaPairRDD<String, TypedRow> toupdateresult,
+            String outputPath,
+            String type) {
         results.leftOuterJoin(toupdateresult)
-                .map(p -> {
+                .map(
+                        p -> {
                             Result r = p._2()._1();
                             if (p._2()._2().isPresent()) {
                                 Set<String> communityList = p._2()._2().get().getAccumulator();
                                 for (Context c : r.getContext()) {
                                     if (communityList.contains(c.getId())) {
-                                //verify if the datainfo for this context contains propagation
-                                if (!c.getDataInfo().stream().map(di -> di.getInferenceprovenance()).collect(Collectors.toSet()).contains(PROPAGATION_DATA_INFO_TYPE)){
-                                    c.getDataInfo().add(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
-                                    //community id already in the context of the result. Remove it from the set that has to be added
+                                        // verify if the datainfo for this context contains
+                                        // propagation
+                                        if (!c.getDataInfo().stream()
+                                                .map(di -> di.getInferenceprovenance())
+                                                .collect(Collectors.toSet())
+                                                .contains(PROPAGATION_DATA_INFO_TYPE)) {
+                                            c.getDataInfo()
+                                                    .add(
+                                                            getDataInfo(
+                                                                    PROPAGATION_DATA_INFO_TYPE,
+                                                                    PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                                                                    PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME));
+                                            // community id already in the context of the result.
+                                            // Remove it from the set that has to be added
                                             communityList.remove(c.getId());
                                         }
                                     }
@@ -439,7 +624,12 @@ public class SparkResultToCommunityThroughSemRelJob3 {
                                 for (String cId : communityList) {
                                     Context context = new Context();
                                     context.setId(cId);
-                            context.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
+                                    context.setDataInfo(
+                                            Arrays.asList(
+                                                    getDataInfo(
+                                                            PROPAGATION_DATA_INFO_TYPE,
+                                                            PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
+                                                            PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
                                     cc.add(context);
                                 }
                                 r.setContext(cc);
@@ -450,13 +640,10 @@ public class SparkResultToCommunityThroughSemRelJob3 {
                 .saveAsTextFile(outputPath + "/" + type);
     }
 
-
-
-    private static TypedRow getTypedRow(List<String> communityIdList, List<Context> context, String id, String type) {
-        Set<String> result_communities = context
-                .stream()
-                .map(c -> c.getId())
-                .collect(Collectors.toSet());
+    private static TypedRow getTypedRow(
+            List<String> communityIdList, List<Context> context, String id, String type) {
+        Set<String> result_communities =
+                context.stream().map(c -> c.getId()).collect(Collectors.toSet());
         TypedRow tp = new TypedRow();
         tp.setSourceId(id);
         tp.setType(type);