changed the save mode to avoid NegativeArraySize... error. Needed to modify also the preparationstep2

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java

@@ -6,6 +6,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.sql.Dataset;
@@ -47,7 +48,7 @@ public class PrepareResultOrcidAssociationStep1 {
         final String resultClassName = parser.get("resultTableName");
         log.info("resultTableName: {}", resultClassName);
 
-        final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrel").split(";"));
+        final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
         log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
 
         final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
@@ -76,7 +77,7 @@ public class PrepareResultOrcidAssociationStep1 {
         //read the relation table and the table related to the result it is using
         final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
         org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
-                .map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
+                .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
         relation.createOrReplaceTempView("relation");
 
         log.info("Reading Graph table from: {}", inputPath + "/" + resultType);
@@ -84,7 +85,7 @@ public class PrepareResultOrcidAssociationStep1 {
 
         result.createOrReplaceTempView("result");
 
-        getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath);
+        getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath + "/" + resultType);
 
     }
 
@@ -107,12 +108,15 @@ public class PrepareResultOrcidAssociationStep1 {
 
         spark.sql(query)
                 .as(Encoders.bean(ResultOrcidList.class))
-                .toJSON()
-        .write()
-        .mode(SaveMode.Append)
-        .option("compression","gzip")
-        .text(outputPath)
-        ;
+                .toJavaRDD()
+                .map(r -> OBJECT_MAPPER.writeValueAsString(r))
+                .saveAsTextFile(outputPath, GzipCodec.class);
+//                .toJSON()
+//        .write()
+//        .mode(SaveMode.Append)
+//        .option("compression","gzip")
+//        .text(outputPath)
+//        ;
     }
 
 

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java

@@ -21,7 +21,7 @@ public class PrepareResultOrcidAssociationStep2 {
 
     public static void main(String[] args) throws Exception {
         String jsonConfiguration = IOUtils.toString(SparkOrcidToResultFromSemRelJob3.class
-                .getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult2_parameters.json"));
+                .getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters2.json"));
 
         final ArgumentApplicationParser parser = new ArgumentApplicationParser(
                 jsonConfiguration);
@@ -50,7 +50,10 @@ public class PrepareResultOrcidAssociationStep2 {
 
     private static void mergeInfo(SparkSession spark, String inputPath, String outputPath) {
 
-        Dataset<ResultOrcidList> resultOrcidAssoc = readAssocResultOrcidList(spark, inputPath);
+        Dataset<ResultOrcidList> resultOrcidAssoc = readAssocResultOrcidList(spark, inputPath + "/publication")
+                .union(readAssocResultOrcidList(spark, inputPath + "/dataset"))
+                .union(readAssocResultOrcidList(spark, inputPath + "/otherresearchproduct"))
+                .union(readAssocResultOrcidList(spark, inputPath + "/software"));
 
         resultOrcidAssoc
                 .toJavaRDD()

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java

@@ -0,0 +1,4 @@
+package eu.dnetlib.dhp.resulttocommunityfromorganization;
+
+public class PrepareInfo {
+}

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultCommunityList.java

@@ -0,0 +1,4 @@
+package eu.dnetlib.dhp.resulttocommunityfromorganization;
+
+public class ResultCommunityList {
+}

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/ResultOrganizations.java

@@ -0,0 +1,4 @@
+package eu.dnetlib.dhp.resulttocommunityfromorganization;
+
+public class ResultOrganizations {
+}

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob2.java

@@ -0,0 +1,390 @@
+package eu.dnetlib.dhp.resulttocommunityfromorganization;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.gson.Gson;
+import eu.dnetlib.dhp.TypedRow;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Encoders;
+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 SparkResultToCommunityFromOrganization {
+
+    public static void main(String[] args) throws Exception {
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToCommunityFromOrganization.class.getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromorganization/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()
+                .appName(SparkResultToCommunityFromOrganization.class.getSimpleName())
+                .master(parser.get("master"))
+                .config(conf)
+                .enableHiveSupport()
+                .getOrCreate();
+
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+        final String inputPath = parser.get("sourcePath");
+        final String outputPath = "/tmp/provision/propagation/communitytoresult";
+        final OrganizationMap organizationMap = new Gson().fromJson(parser.get("organizationtoresultcommunitymap"), OrganizationMap.class);
+        boolean writeUpdates = TRUE.equals(parser.get("writeUpdate"));
+        boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
+
+        System.out.println(new Gson().toJson(organizationMap));
+
+        createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
+
+        JavaRDD<Relation> relations_rdd_all = sc.textFile(inputPath + "/relation")
+                .map(item -> new ObjectMapper().readValue(item, Relation.class));
+        JavaRDD<Publication> publications_rdd_all = sc.textFile(inputPath + "/publication")
+                .map(item -> new ObjectMapper().readValue(item, Publication.class));
+        JavaRDD<Dataset> dataset_rdd_all = sc.textFile(inputPath + "/dataset")
+                .map(item -> new ObjectMapper().readValue(item, Dataset.class));
+        JavaRDD<OtherResearchProduct> orp_rdd_all = sc.textFile(inputPath + "/otheresearchproduct")
+                .map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class));
+        JavaRDD<Software> software_rdd_all = sc.textFile(inputPath + "/software")
+                .map(item -> new ObjectMapper().readValue(item, Software.class));
+
+        org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(relations_rdd_all.rdd(), Encoders.bean(Relation.class));
+
+        relation.createOrReplaceTempView("relation");
+//        String query = "SELECT source, target" +
+//                "       FROM relation " +
+//                "       WHERE datainfo.deletedbyinference = false " +
+//                "       AND relClass = '" + RELATION_RESULT_ORGANIZATION_REL_CLASS + "'";
+//
+//        org.apache.spark.sql.Dataset<Row> result_organization = spark.sql(query);
+//        result_organization.createOrReplaceTempView("result_organization");
+//
+//        query = "SELECT source, target " +
+//                "FROM relation " +
+//                "WHERE datainfo.deletedbyinference = false " +
+//                "AND relClass = '" + RELATION_REPRESENTATIVERESULT_RESULT_CLASS + "'" ;
+
+        String query = "SELECT result_organization.source, result_organization.target, org_set  " +
+                "FROM (SELECT source, target " +
+                "      FROM relation " +
+                "      WHERE datainfo.deletedbyinference = false " +
+                "      AND relClass = '" + RELATION_RESULT_ORGANIZATION_REL_CLASS + "') result_organization " +
+                "LEFT JOIN (SELECT source, collect_set(target) org_set " +
+                "      FROM relation " +
+                "      WHERE datainfo.deletedbyinference = false " +
+                "      AND relClass = '" + RELATION_REPRESENTATIVERESULT_RESULT_CLASS + "' " +
+                "      GROUP BY source) organization_organization " +
+                "ON result_organization.target = organization_organization.source ";
+
+        org.apache.spark.sql.Dataset<Row> result_organizationset = spark.sql(query);
+
+        JavaPairRDD<String,TypedRow> result_communitySet = result_organizationset.toJavaRDD().map(r -> {
+            String rId = r.getString(0);
+            List<String> orgs = r.getList(2);
+            String oTarget = r.getString(1);
+            TypedRow tp = new TypedRow();
+            if (organizationMap.containsKey(oTarget)) {
+                    tp.addAll(organizationMap.get(oTarget));
+            }
+            try{
+                for (String oId : orgs) {
+                    if (organizationMap.containsKey(oId)) {
+                        tp.addAll(organizationMap.get(oId));
+                    }
+                }
+            }
+            catch(Exception e){
+                //System.out.println("organizationTargetID: " + oTarget);
+            }
+
+            if(tp.getAccumulator() == null ){
+                return null;
+            }
+            tp.setSourceId(rId);
+
+
+            return tp;
+        })
+                .filter(tr -> !(tr==null))
+                .mapToPair(toPair()).cache();
+
+        if(writeUpdates){
+            result_communitySet.map(c->new ObjectMapper().writeValueAsString(c)).saveAsTextFile(outputPath +"/result_communityset");
+        }
+
+        if(saveGraph){
+            updatePublicationResult(publications_rdd_all, result_communitySet)
+                    .map(p -> new ObjectMapper().writeValueAsString(p))
+                    .saveAsTextFile(outputPath + "/publication");
+
+            updateDatasetResult(dataset_rdd_all, result_communitySet)
+                    .map(p -> new ObjectMapper().writeValueAsString(p))
+                    .saveAsTextFile(outputPath + "/dataset");
+
+            updateORPResult(orp_rdd_all, result_communitySet)
+                    .map(p -> new ObjectMapper().writeValueAsString(p))
+                    .saveAsTextFile(outputPath + "/otherresearchproduct");
+
+            updateSoftwareResult(software_rdd_all, result_communitySet)
+                    .map(p -> new ObjectMapper().writeValueAsString(p))
+                    .saveAsTextFile(outputPath + "/software");
+        }
+
+
+        //relations between organziations and results
+//        JavaPairRDD<String, TypedRow> organization_result = relations
+//                .filter(r -> !r.getDataInfo().getDeletedbyinference())
+//                .filter(r -> RELATION_RESULT_ORGANIZATION_REL_CLASS.equals(r.getRelClass())
+//                        && RELATION_RESULTORGANIZATION_REL_TYPE.equals(r.getRelType()))
+//                .map(r -> {
+//                    TypedRow tp = new TypedRow();
+//                    tp.setSourceId(r.getTarget());
+//                    tp.setTargetId(r.getSource() );
+//                    return tp;
+//                })
+//                .mapToPair(toPair());
+
+        //relations between representative organization and merged Id. One relation per merged organization
+//        JavaPairRDD<String, TypedRow> organization_organization = relations
+//                .filter(r -> !r.getDataInfo().getDeletedbyinference())
+//                .filter( r -> RELATION_ORGANIZATIONORGANIZATION_REL_TYPE.equals(r.getRelType())
+//                        && RELATION_REPRESENTATIVERESULT_RESULT_CLASS.equals(r.getRelClass()))
+//                .map(r -> {
+//                    TypedRow tp = new TypedRow();
+//                    tp.setSourceId(r.getSource());
+//                    tp.setTargetId(r.getTarget());
+//                    return tp;
+//                })
+//                .mapToPair(toPair());
+
+        //get the original id of the organizations to be checked against the id associated to the communities
+//        JavaPairRDD<String, TypedRow> organizationoriginal_result = organization_result.leftOuterJoin(organization_organization)
+//                .map(c -> {
+//                    if (!c._2()._2().isPresent())
+//                        return c._2()._1();
+//                    return c._2()._1().setSourceId(c._2()._2().get().getTargetId());
+//                })
+//                .mapToPair(toPair());
+
+        //associates to each result connected to an organization the list of communities related to that organization
+//        JavaPairRDD<String, TypedRow> to_add_result_communities = organizationoriginal_result.map(o -> {
+//            List<String> communityList = organizationMap.get(o._1());
+//            if (communityList.size() == 0)
+//                return null;
+//            TypedRow tp = o._2();
+//            tp.setAccumulator(new HashSet<>(communityList));
+//            tp.setSourceId(tp.getTargetId());
+//            return tp;
+//        })
+//                .filter(r -> !(r == null))
+//                .mapToPair(toPair())
+//                .reduceByKey((a, b) -> {
+//                    if (a == null)
+//                        return b;
+//                    if (b == null)
+//                        return a;
+//                    a.addAll(b.getAccumulator());
+//                    return a;
+//                });
+
+
+//        JavaRDD<Publication> publications = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
+//                .map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class)).cache();
+//        JavaRDD<Dataset> datasets = sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
+//                .map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class)).cache();
+//        JavaRDD<Software> software = sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
+//                .map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class)).cache();
+//        JavaRDD<OtherResearchProduct> other = sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
+//                .map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class)).cache();
+//
+//        JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
+//        JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
+//        JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
+//        JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
+//
+//        updateResultForCommunity(pubs, to_add_result_communities, outputPath, "publication", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
+//        updateResultForCommunity(dss, to_add_result_communities, outputPath, "dataset", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
+//        updateResultForCommunity(sfw, to_add_result_communities, outputPath, "software", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
+//        updateResultForCommunity(orp, to_add_result_communities, outputPath, "otherresearchproduct", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
+
+    }
+
+    private static JavaRDD<Publication> updatePublicationResult(JavaRDD<Publication> result, JavaPairRDD<String, TypedRow> result_communitySet){
+        JavaRDD<Result> tmp = result.map(r -> (Result)r);
+        return updateResultDataset(tmp, result_communitySet).map(r -> (Publication)r);
+
+    }
+    private static JavaRDD<Dataset> updateDatasetResult(JavaRDD<Dataset> result, JavaPairRDD<String, TypedRow> result_communitySet){
+        JavaRDD<Result> tmp = result.map(r -> (Result)r);
+        return updateResultDataset(tmp, result_communitySet).map(r -> (Dataset) r);
+
+    }
+    private static JavaRDD<OtherResearchProduct> updateORPResult(JavaRDD<OtherResearchProduct> result, JavaPairRDD<String, TypedRow> result_communitySet){
+        JavaRDD<Result> tmp = result.map(r -> (Result)r);
+        return updateResultDataset(tmp, result_communitySet).map(r -> (OtherResearchProduct)r);
+
+    }
+    private static JavaRDD<Software> updateSoftwareResult(JavaRDD<Software> result, JavaPairRDD<String, TypedRow> result_communitySet){
+        JavaRDD<Result> tmp = result.map(r -> (Result)r);
+        return updateResultDataset(tmp, result_communitySet).map(r -> (Software) r);
+
+    }
+    private  static JavaRDD<Result> updateResultDataset(JavaRDD<Result> result, JavaPairRDD<String, TypedRow> result_communitySet){
+        return result.mapToPair(p -> new Tuple2<>(p.getId(),p)).leftOuterJoin(result_communitySet)
+                .map(c -> {
+                    Result r = c._2()._1();
+                    if(c._2()._2().isPresent()){
+                        Set<String> communitySet = c._2()._2().get().getAccumulator();
+                        List<String> contextList = r.getContext().stream().map(con -> con.getId()).collect(Collectors.toList());
+                        for(String cId:communitySet){
+                            if(!contextList.contains(cId)){
+                                Context newContext = new Context();
+                                newContext.setId(cId);
+                                newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE,
+                                        PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME)));
+                                r.getContext().add(newContext);
+                            }
+                        }
+                    }
+                    return r;
+                });
+
+    }
+    //   private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
+//        results.leftOuterJoin(toupdateresult)
+//                .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_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_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());
+//                                }
+//                            }
+//                        }
+//                        List<Context> cc = r.getContext();
+//                        for(String cId: communityList){
+//                            Context context = new Context();
+//                            context.setId(cId);
+//                            context.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME)));
+//                            cc.add(context);
+//                        }
+//                        r.setContext(cc);
+//                    }
+//                    return r;
+//                })
+//                .map(p -> new ObjectMapper().writeValueAsString(p))
+//                .saveAsTextFile(outputPath+"/"+type);
+//    }
+
+
+}
+
+
+/*
+package eu.dnetlib.data.mapreduce.hbase.propagation.communitythroughorganization;
+
+import com.google.gson.Gson;
+import eu.dnetlib.data.mapreduce.hbase.propagation.Value;
+import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder;
+import eu.dnetlib.data.proto.OafProtos;
+import eu.dnetlib.data.proto.TypeProtos;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.hadoop.hbase.client.Result;
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
+import org.apache.hadoop.hbase.mapreduce.TableMapper;
+import org.apache.hadoop.hbase.util.Bytes;
+import org.apache.hadoop.io.Text;
+
+import java.io.IOException;
+import java.util.Set;
+
+import static eu.dnetlib.data.mapreduce.hbase.propagation.PropagationConstants.*;
+import static eu.dnetlib.data.mapreduce.hbase.propagation.Utils.getEntity;
+import static eu.dnetlib.data.mapreduce.hbase.propagation.Utils.getRelationTarget;
+
+public class PropagationCommunityThroughOrganizationMapper extends TableMapper<ImmutableBytesWritable, Text> {
+    private Text valueOut;
+    private ImmutableBytesWritable keyOut;
+    private OrganizationMap organizationMap;
+
+    //seleziono il tipo della entry:
+    //Result:
+    //se non e' deleted by inference ed ha organizzazioni a cui e' associato,
+    // //emetto id della relazione ed id del risultato per ogni organizzazione a cui e' associato
+    //ORGANIZATION:
+    //se non e' deleted by inference e non e' deduplicata emetto l'id della organizzazione
+    //se non e' deleted by inference ed e' deduplicata, emetto id della organizzazione ed id del deduplicato e lista delle organizzazioni mergiate
+    @Override
+    protected void setup(final Context context) throws IOException, InterruptedException {
+        super.setup(context);
+        valueOut = new Text();
+        keyOut = new ImmutableBytesWritable();
+        organizationMap = new Gson().fromJson(context.getConfiguration().get("organizationtoresult.community.map"), OrganizationMap.class);
+        System.out.println("got organizationtoresult map: " + new Gson().toJson(organizationMap)) ;
+    }
+
+    @Override
+    protected void map(final ImmutableBytesWritable keyIn, final Result value, final Context context) throws IOException, InterruptedException {
+        final TypeProtos.Type type = OafRowKeyDecoder.decode(keyIn.copyBytes()).getType();
+        final OafProtos.OafEntity entity = getEntity(value, type);//getEntity already verified that it is not delByInference
+        if (entity != null) {
+            switch (type) {
+                case organization:
+                    DedupedList communityList = getCommunityList(Bytes.toString(keyIn.get()),
+                            getRelationTarget(value, DEDUP_RELATION_ORGANIZATION + REL_DEDUP_REPRESENTATIVE_RESULT, context, COUNTER_PROPAGATION), context);
+                    if (communityList.size() > 0){
+                        valueOut.set(Value.newInstance(
+                                new Gson().toJson(
+                                        communityList, //search for organizationtoresult it merges
+                                        DedupedList.class),
+                                ORGANIZATION_COMMUNITY_TRUST,
+                                Type.fromorganization).toJson());
+                        context.write(keyIn, valueOut);
+                        context.getCounter(COUNTER_PROPAGATION, "emit for organizationtoresult ").increment(1);
+                    }else{
+                        context.getCounter(COUNTER_PROPAGATION, "community list size = 0 ").increment(1);
+                    }
+
+                    break;
+                case result:
+                    Set<String> result_organization = getRelationTarget(value, RELATION_ORGANIZATION + REL_RESULT_ORGANIZATION, context, COUNTER_PROPAGATION);
+                    for(String org: result_organization)
+                        emit(org, Bytes.toString(keyIn.get()), context);
+                    break;
+            }
+        }
+    }
+
+    private DedupedList getCommunityList(String organizationId, Set<String> relationTarget, Context context) {
+        DedupedList communityList = new DedupedList();
+        relationTarget.stream().forEach(org -> communityList.addAll(organizationMap.get(StringUtils.substringAfter(org, "|"))));
+        communityList.addAll(organizationMap.get(StringUtils.substringAfter(organizationId,"|")));
+        communityList.stream().forEach(c->context.getCounter(COUNTER_PROPAGATION,"found organizationtoresult for " + c).increment(1));
+        return communityList;
+    }
+
+    private void emit(String org, String resId, Context context) throws IOException, InterruptedException {
+        keyOut.set(Bytes.toBytes(org));
+        valueOut.set(Value.newInstance(resId, ORGANIZATION_COMMUNITY_TRUST, Type.fromresult).toJson());
+        context.write(keyOut,valueOut);
+        context.getCounter(COUNTER_PROPAGATION, "emit for result").increment(1);
+    }
+
+}
+ */

dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java

@@ -0,0 +1,4 @@
+package eu.dnetlib.dhp.orcidtoresultfromsemrel;
+
+public class OrcidPropagationJobTest {
+}