changed relclass and reltype in reelation specification for country propagation and implementation of propagation of result affiliation through institutional repositories

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java

@@ -1,6 +1,7 @@
 package eu.dnetlib.dhp.countrypropagation;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.TypedRow;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.Dataset;
@@ -9,13 +10,14 @@ import org.apache.hadoop.io.Text;
 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.api.java.function.PairFunction;
 import org.apache.spark.sql.*;
 import scala.Tuple2;
 
 import java.io.File;
 import java.util.*;
 
+import static eu.dnetlib.dhp.PropagationConstant.*;
+
 public class SparkCountryPropagationJob {
     public static void main(String[] args) throws Exception {
 
@@ -51,9 +53,10 @@ public class SparkCountryPropagationJob {
         JavaPairRDD<String, TypedRow> organization_datasource = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
                 .map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class))
                 .filter(r -> !r.getDataInfo().getDeletedbyinference())
-                .filter(r -> "datasourceOrganization".equals(r.getRelClass()) && "isProvidedBy".equals(r.getRelType()))
+                .filter(r -> RELATION_DATASOURCEORGANIZATION_REL_TYPE.equals(r.getRelClass()) && RELATION_ORGANIZATION_DATASOURCE_REL_CLASS.equals(r.getRelType()))
                 .map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
-                .mapToPair(toPair());
+                .mapToPair(toPair()); //id is the organization identifier
+
 
         JavaPairRDD<String, TypedRow> datasources = sc.sequenceFile(inputPath + "/datasource", Text.class, Text.class)
                 .map(item -> new ObjectMapper().readValue(item._2().toString(), Datasource.class))
@@ -72,7 +75,7 @@ public class SparkCountryPropagationJob {
                 .map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class));
 
         JavaPairRDD<String, TypedRow> datasource_results = publications
-                .map(oaf -> getTypedRows(oaf))
+                .map(oaf -> getTypedRowsDatasourceResult(oaf))
                 .flatMapToPair(f -> {
                     ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
                     for (TypedRow t : f) {
@@ -81,7 +84,7 @@ public class SparkCountryPropagationJob {
                     return ret.iterator();
                 })
                 .union(datasets
-                        .map(oaf -> getTypedRows(oaf))
+                        .map(oaf -> getTypedRowsDatasourceResult(oaf))
                         .flatMapToPair(f -> {
                             ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
                             for (TypedRow t : f) {
@@ -90,7 +93,7 @@ public class SparkCountryPropagationJob {
                             return ret.iterator();
                         }))
                 .union(software
-                .map(oaf -> getTypedRows(oaf))
+                .map(oaf -> getTypedRowsDatasourceResult(oaf))
                 .flatMapToPair(f -> {
                     ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
                     for (TypedRow t : f) {
@@ -99,7 +102,7 @@ public class SparkCountryPropagationJob {
                     return ret.iterator();
                 }))
                 .union(other
-                        .map(oaf -> getTypedRows(oaf))
+                        .map(oaf -> getTypedRowsDatasourceResult(oaf))
                         .flatMapToPair(f -> {
                             ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
                             for (TypedRow t : f) {
@@ -155,55 +158,53 @@ public class SparkCountryPropagationJob {
         results.leftOuterJoin(toupdateresult)
                 .map(c -> {
                     OafEntity oaf = c._2()._1();
-                    List<Qualifier> qualifierList = null;
+                    List<Country> countryList = null;
                     if (oaf.getClass() == Publication.class) {
-                        qualifierList = ((Publication) oaf).getCountry();
+                        countryList = ((Publication) oaf).getCountry();
 
                     }
                     if (oaf.getClass() == Dataset.class){
-                        qualifierList = ((Dataset) oaf).getCountry();
+                        countryList = ((Dataset) oaf).getCountry();
                     }
 
                     if (oaf.getClass() == Software.class){
-                        qualifierList = ((Software) oaf).getCountry();
+                        countryList = ((Software) oaf).getCountry();
                     }
 
                     if (oaf.getClass() == OtherResearchProduct.class){
-                        qualifierList = ((OtherResearchProduct) oaf).getCountry();
+                        countryList = ((OtherResearchProduct) oaf).getCountry();
                     }
 
                     if (c._2()._2().isPresent()) {
                         HashSet<String> countries = new HashSet<>();
-                        for (Qualifier country : qualifierList) {
+                        for (Qualifier country : countryList) {
                             countries.add(country.getClassid());
                         }
                         TypedRow t = c._2()._2().get();
 
                         for (String country : t.getCountry().split(";")) {
                             if (!countries.contains(country)) {
-                                Qualifier q = new Qualifier();
+                                countryList.add(getCountry(country));
-                                q.setClassid(country);
-                                qualifierList.add(q);
                             }
 
                         }
                         if (oaf.getClass() == Publication.class) {
-                            ((Publication) oaf).setCountry(qualifierList);
+                            ((Publication) oaf).setCountry(countryList);
                             return (Publication) oaf;
 
                         }
                         if (oaf.getClass() == Dataset.class){
-                            ((Dataset) oaf).setCountry(qualifierList);
+                            ((Dataset) oaf).setCountry(countryList);
                             return (Dataset) oaf;
                         }
 
                         if (oaf.getClass() == Software.class){
-                          ((Software) oaf).setCountry(qualifierList);
+                          ((Software) oaf).setCountry(countryList);
                             return (Software) oaf;
                         }
 
                         if (oaf.getClass() == OtherResearchProduct.class){
-                           ((OtherResearchProduct) oaf).setCountry(qualifierList);
+                           ((OtherResearchProduct) oaf).setCountry(countryList);
                             return (OtherResearchProduct) oaf;
                         }
                     }
@@ -215,40 +216,7 @@ public class SparkCountryPropagationJob {
                 .saveAsTextFile(outputPath+"/"+type);
     }
 
-    private static List<TypedRow> getTypedRows(OafEntity oaf) {
-        List<TypedRow> lst = new ArrayList<>();
-        Set<String> datasources_provenance = new HashSet<>();
-        List<Instance> instanceList = null;
-        String type = "";
-        if (oaf.getClass() == Publication.class) {
-            instanceList = ((Publication) oaf).getInstance();
-            type = "publication";
-        }
-        if (oaf.getClass() == Dataset.class){
-            instanceList = ((Dataset)oaf).getInstance();
-            type = "dataset";
-        }
 
-        if (oaf.getClass() == Software.class){
-            instanceList = ((Software)oaf).getInstance();
-            type = "software";
-        }
-
-        if (oaf.getClass() == OtherResearchProduct.class){
-            instanceList = ((OtherResearchProduct)oaf).getInstance();
-            type = "otherresearchproduct";
-        }
-
-
-        for (Instance i : instanceList) {
-            datasources_provenance.add(i.getCollectedfrom().getKey());
-            datasources_provenance.add(i.getHostedby().getKey());
-        }
-        for (String dsId : datasources_provenance) {
-            lst.add(new TypedRow().setSourceId(dsId).setTargetId(oaf.getId()).setType(type));
-        }
-        return lst;
-    }
 
 
     private static JavaPairRDD<String, TypedRow> getResults(JavaSparkContext sc , String inputPath){
@@ -280,10 +248,6 @@ public class SparkCountryPropagationJob {
 
 
 
-    private static PairFunction<TypedRow, String, TypedRow> toPair() {
-        return e -> new Tuple2<>( e.getSourceId(), e);
-
-        };
 
 
 }

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java

@@ -1,11 +1,22 @@
 package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
 
+import eu.dnetlib.dhp.TypedRow;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import org.apache.commons.io.IOUtils;
+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.SparkSession;
-
+import org.apache.hadoop.io.Text;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import eu.dnetlib.dhp.schema.oaf.*;
+import scala.Tuple2;
+
+import static eu.dnetlib.dhp.PropagationConstant.*;
 
 public class SparkResultToOrganizationFromIstRepoJob {
     public static void main(String[] args) throws Exception {
@@ -28,78 +39,28 @@ public class SparkResultToOrganizationFromIstRepoJob {
         if (!directory.exists()) {
             directory.mkdirs();
         }
-    }
-    }
-/*
-package eu.dnetlib.dhp.countrypropagation;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.Dataset;
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.io.Text;
-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.api.java.Optional;
-import org.apache.spark.api.java.function.Function2;
-import org.apache.spark.api.java.function.PairFunction;
-import org.apache.spark.rdd.RDD;
-import org.apache.spark.sql.*;
-import scala.Tuple2;
-
-import java.io.File;
-import java.util.*;
-import java.util.stream.Stream;
-
-public class SparkCountryPropagationJob {
-    public static void main(String[] args) throws Exception {
-
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCountryPropagationJob.class.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json")));
-        parser.parseArgument(args);
-        final SparkSession spark = SparkSession
-                .builder()
-                .appName(SparkCountryPropagationJob.class.getSimpleName())
-                .master(parser.get("master"))
-                .enableHiveSupport()
-                .getOrCreate();
-
-        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
-        final String inputPath = parser.get("sourcePath");
-        final String outputPath = "/tmp/provision/propagation/countrytoresultfrominstitutionalrepositories";
-
-        File directory = new File(outputPath);
-
-        if(!directory.exists()){
-            directory.mkdirs();
-        }
-
-        //TODO: add as Job Parameters
-        List<String> whitelist = Arrays.asList("10|opendoar____::300891a62162b960cf02ce3827bb363c");
-        List<String> allowedtypes = Arrays.asList("pubsrepository::institutional");
-
-
-        JavaPairRDD<String, TypedRow> organizations = sc.sequenceFile(inputPath + "/organization", Text.class, Text.class)
-                .map(item -> new ObjectMapper().readValue(item._2().toString(), Organization.class))
-                .filter(org -> !org.getDataInfo().getDeletedbyinference())
-                .map(org -> new TypedRow().setSourceId(org.getId()).setCountry(org.getCountry().getClassid()))
-                .mapToPair(toPair());
-
-        JavaPairRDD<String, TypedRow> organization_datasource = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
-                .map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class))
-                .filter(r -> !r.getDataInfo().getDeletedbyinference())
-                .filter(r -> "datasourceOrganization".equals(r.getRelClass()) && "isProvidedBy".equals(r.getRelType()))
-                .map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
-                .mapToPair(toPair());
 
+        //get the institutional repositories
         JavaPairRDD<String, TypedRow> datasources = sc.sequenceFile(inputPath + "/datasource", Text.class, Text.class)
                 .map(item -> new ObjectMapper().readValue(item._2().toString(), Datasource.class))
-                .filter(ds -> whitelist.contains(ds.getId()) || allowedtypes.contains(ds.getDatasourcetype().getClassid()))
+                .filter(ds -> INSTITUTIONAL_REPO_TYPE.equals(ds.getDatasourcetype().getClassid()))
                 .map(ds -> new TypedRow().setSourceId(ds.getId()))
                 .mapToPair(toPair());
 
 
+        JavaPairRDD<String, TypedRow> rel_datasource_organization = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
+                .map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class))
+                .filter(r -> !r.getDataInfo().getDeletedbyinference())
+                .filter(r -> RELATION_DATASOURCEORGANIZATION_REL_TYPE.equals(r.getRelClass()) && RELATION_DATASOURCE_ORGANIZATION_REL_CLASS.equals(r.getRelType()))
+                .map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
+                .mapToPair(toPair());
+
+        JavaPairRDD<String, TypedRow> instdatasource_organization = datasources.join(rel_datasource_organization)
+                .map(x -> x._2()._2())
+                .mapToPair(toPair());
+
+        JavaRDD<Relation> relations = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
+                .map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class));
         JavaRDD<Publication> publications = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
                 .map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class));
         JavaRDD<Dataset> datasets = sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
@@ -110,7 +71,7 @@ public class SparkCountryPropagationJob {
                 .map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class));
 
         JavaPairRDD<String, TypedRow> datasource_results = publications
-                .map(oaf -> getTypedRows(oaf))
+                .map(oaf -> getTypedRowsDatasourceResult(oaf))
                 .flatMapToPair(f -> {
                     ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
                     for (TypedRow t : f) {
@@ -119,7 +80,7 @@ public class SparkCountryPropagationJob {
                     return ret.iterator();
                 })
                 .union(datasets
-                        .map(oaf -> getTypedRows(oaf))
+                        .map(oaf -> getTypedRowsDatasourceResult(oaf))
                         .flatMapToPair(f -> {
                             ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
                             for (TypedRow t : f) {
@@ -128,7 +89,7 @@ public class SparkCountryPropagationJob {
                             return ret.iterator();
                         }))
                 .union(software
-                .map(oaf -> getTypedRows(oaf))
+                        .map(oaf -> getTypedRowsDatasourceResult(oaf))
                         .flatMapToPair(f -> {
                             ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
                             for (TypedRow t : f) {
@@ -137,7 +98,7 @@ public class SparkCountryPropagationJob {
                             return ret.iterator();
                         }))
                 .union(other
-                        .map(oaf -> getTypedRows(oaf))
+                        .map(oaf -> getTypedRowsDatasourceResult(oaf))
                         .flatMapToPair(f -> {
                             ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
                             for (TypedRow t : f) {
@@ -146,185 +107,23 @@ public class SparkCountryPropagationJob {
                             return ret.iterator();
                         }));
 
-        JavaPairRDD<String, OafEntity> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
+        JavaRDD<Relation> newRels = instdatasource_organization.join(datasource_results)
-        JavaPairRDD<String, OafEntity> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
+                .flatMap(c -> {
-        JavaPairRDD<String, OafEntity> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
+                    List<Relation> rels = new ArrayList();
-        JavaPairRDD<String, OafEntity> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
+                    rels.add(getRelation(c._2()._1().getTargetId(), c._2()._2().getTargetId(), RELATION_ORGANIZATION_RESULT_REL_CLASS,
-
+                            RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
-        JavaPairRDD<String, TypedRow> datasource_country = organizations.join(organization_datasource)
+                            PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
-                .map(x -> x._2()._1().setSourceId(x._2()._2().getTargetId())) // (OrganizationId,(TypedRow for Organization, TypedRow for Relation)
+                    rels.add(getRelation(c._2()._2().getTargetId(), c._2()._1().getTargetId(), RELATION_ORGANIZATION_RESULT_REL_CLASS,
-                .mapToPair(toPair()); //(DatasourceId, TypedRowforOrganziation)
+                            RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
-
+                            PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
-
+                    return rels.iterator();
-        JavaPairRDD<String, TypedRow> alloweddatasources_country = datasources.join(datasource_country)
-                .mapToPair(ds -> new Tuple2<>(ds._1(), ds._2()._2()));
-
-
-        JavaPairRDD<String,TypedRow> toupdateresult = alloweddatasources_country.join(datasource_results)
-                .map(u -> u._2()._2().setCountry(u._2()._1().getCountry()))
-                .mapToPair(toPair())
-                .reduceByKey((a, p) -> {
-                    if (a == null) {
-                        return p;
-                    }
-                    if (p == null) {
-                        return a;
-                    }
-                    HashSet<String> countries = new HashSet();
-                    countries.addAll(Arrays.asList(a.getCountry().split(";")));
-                    countries.addAll(Arrays.asList(p.getCountry().split(";")));
-                    String country = new String();
-                    for (String c : countries) {
-                        country += c + ";";
-                    }
-
-                    return a.setCountry(country);
                 });
+        newRels.map(p -> new ObjectMapper().writeValueAsString(p))
+                .saveAsTextFile(outputPath + "/relation_new");
 
-        updateResult(pubs, toupdateresult, outputPath, "publication");
+        newRels.union(relations).map(p -> new ObjectMapper().writeValueAsString(p))
-        updateResult(dss, toupdateresult, outputPath, "dataset");
+                .saveAsTextFile(outputPath + "/relation");
-        updateResult(sfw, toupdateresult, outputPath, "software");
-        updateResult(orp, toupdateresult, outputPath, "otherresearchproduct");
-        //we use leftOuterJoin because we want to rebuild the entire structure
-
-    }
-
-    private static void updateResult(JavaPairRDD<String, OafEntity> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
-        results.leftOuterJoin(toupdateresult)
-                .map(c -> {
-                    OafEntity oaf = c._2()._1();
-                    List<Qualifier> qualifierList = null;
-                    if (oaf.getClass() == Publication.class) {
-                        qualifierList = ((Publication) oaf).getCountry();
-
-                    }
-                    if (oaf.getClass() == Dataset.class){
-                        qualifierList = ((Dataset) oaf).getCountry();
-                    }
-
-                    if (oaf.getClass() == Software.class){
-                        qualifierList = ((Software) oaf).getCountry();
-                    }
-
-                    if (oaf.getClass() == OtherResearchProduct.class){
-                        qualifierList = ((OtherResearchProduct) oaf).getCountry();
-                    }
-
-                    if (c._2()._2().isPresent()) {
-                        HashSet<String> countries = new HashSet<>();
-                        for (Qualifier country : qualifierList) {
-                            countries.add(country.getClassid());
-                        }
-                        TypedRow t = c._2()._2().get();
-
-                        for (String country : t.getCountry().split(";")) {
-                            if (!countries.contains(country)) {
-                                Qualifier q = new Qualifier();
-                                q.setClassid(country);
-                                qualifierList.add(q);
-                            }
-
-                        }
-                        if (oaf.getClass() == Publication.class) {
-                            ((Publication) oaf).setCountry(qualifierList);
-                            return (Publication) oaf;
-
-                        }
-                        if (oaf.getClass() == Dataset.class){
-                            ((Dataset) oaf).setCountry(qualifierList);
-                            return (Dataset) oaf;
-                        }
-
-                        if (oaf.getClass() == Software.class){
-                          ((Software) oaf).setCountry(qualifierList);
-                            return (Software) oaf;
-                        }
-
-                        if (oaf.getClass() == OtherResearchProduct.class){
-                           ((OtherResearchProduct) oaf).setCountry(qualifierList);
-                            return (OtherResearchProduct) oaf;
-                        }
     }
 
 
-                    return null;
-                })
-                .map(p -> new ObjectMapper().writeValueAsString(p))
-                .saveAsTextFile(outputPath+"/"+type);
 }
-
-    private static List<TypedRow> getTypedRows(OafEntity oaf) {
-        List<TypedRow> lst = new ArrayList<>();
-        Set<String> datasources_provenance = new HashSet<>();
-        List<Instance> instanceList = null;
-        String type = "";
-        if (oaf.getClass() == Publication.class) {
-            instanceList = ((Publication) oaf).getInstance();
-            type = "publication";
-        }
-        if (oaf.getClass() == Dataset.class){
-            instanceList = ((Dataset)oaf).getInstance();
-            type = "dataset";
-        }
-
-        if (oaf.getClass() == Software.class){
-            instanceList = ((Software)oaf).getInstance();
-            type = "software";
-        }
-
-        if (oaf.getClass() == OtherResearchProduct.class){
-            instanceList = ((OtherResearchProduct)oaf).getInstance();
-            type = "otherresearchproduct";
-        }
-
-
-        for (Instance i : instanceList) {
-            datasources_provenance.add(i.getCollectedfrom().getKey());
-            datasources_provenance.add(i.getHostedby().getKey());
-        }
-        for (String dsId : datasources_provenance) {
-            lst.add(new TypedRow().setSourceId(dsId).setTargetId(oaf.getId()).setType(type));
-        }
-        return lst;
-    }
-
-
-    private static JavaPairRDD<String, TypedRow> getResults(JavaSparkContext sc , String inputPath){
-
-        return
-                sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
-                    .map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class))
-                        .filter(ds -> !ds.getDataInfo().getDeletedbyinference())
-                    .map(oaf -> new TypedRow().setType("dataset").setSourceId(oaf.getId()))
-                    .mapToPair(toPair())
-                .union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
-                        .map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class))
-                        .filter(o -> !o.getDataInfo().getDeletedbyinference())
-                        .map(oaf -> new TypedRow().setType("otherresearchproduct").setSourceId(oaf.getId()))
-                        .mapToPair(toPair()))
-                .union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
-                        .map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class))
-                        .filter(s -> !s.getDataInfo().getDeletedbyinference())
-                        .map(oaf -> new TypedRow().setType("software").setSourceId(oaf.getId()))
-                        .mapToPair(toPair()))
-                .union(sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
-                                .map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class))
-                        .filter(p -> !p.getDataInfo().getDeletedbyinference())
-                                .map(oaf -> new TypedRow().setType("publication").setSourceId(oaf.getId()))
-                                .mapToPair(toPair()));
-
-
-    }
-
-
-
-    private static PairFunction<TypedRow, String, TypedRow> toPair() {
-        return e -> new Tuple2<>( e.getSourceId(), e);
-
-        };
-
-
-}
-
-
- */