refactoring

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java

@@ -1,11 +1,7 @@
+
 package eu.dnetlib.dhp.oa.graph.dump.community;
 
-import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
-import org.apache.spark.SparkConf;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
 
 import java.io.Serializable;
 import java.util.Objects;
@@ -13,11 +9,16 @@ import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+
+import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
 
 public class CommunitySplit implements Serializable {
 
-
 	public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, CommunityMap communityMap) {
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java

@@ -25,8 +25,8 @@ import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
-import eu.dnetlib.dhp.schema.dump.oaf.community.Funder;
 import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
+import eu.dnetlib.dhp.schema.dump.oaf.community.Funder;
 import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.Relation;

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java

@@ -64,16 +64,10 @@ public class SparkSplitForCommunity implements Serializable {
 
 		split.run(isSparkSessionManaged, inputPath, outputPath, communityMap);
 
-
-
-
 	}
 
 	public static ISLookUpService getIsLookUpService(String isLookUpUrl) {
 		return ISLookupClientFactory.getLookUpService(isLookUpUrl);
 	}
 
-
-
-
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java

@@ -19,7 +19,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
-
 import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
 
 public class SparkUpdateProjectInfo implements Serializable {

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextEntities.java

@@ -46,7 +46,6 @@ public class CreateContextEntities implements Serializable {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
 		parser.parseArgument(args);
 
-
 		final String hdfsPath = parser.get("hdfsPath");
 		log.info("hdfsPath: {}", hdfsPath);
 
@@ -90,8 +89,6 @@ public class CreateContextEntities implements Serializable {
 		queryInformationSystem.getContextInformation(consumer);
 	}
 
-
-
 	protected <R extends ResearchInitiative> void writeEntity(final R r) {
 		try {
 			writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r));

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextRelation.java

@@ -11,7 +11,6 @@ import java.util.Optional;
 import java.util.function.Consumer;
 import java.util.function.Function;
 
-import eu.dnetlib.dhp.schema.oaf.Datasource;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FSDataOutputStream;
@@ -24,6 +23,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
+import eu.dnetlib.dhp.schema.oaf.Datasource;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 
 public class CreateContextRelation implements Serializable {
@@ -66,7 +66,10 @@ public class CreateContextRelation implements Serializable {
 		cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class));
 
 		log.info("Creating relations for projects... ");
-		cce.execute(Process::getRelation, CONTEX_RELATION_PROJECT, ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class));
+		cce
+			.execute(
+				Process::getRelation, CONTEX_RELATION_PROJECT,
+				ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class));
 
 	}
 
@@ -92,14 +95,14 @@ public class CreateContextRelation implements Serializable {
 
 	}
 
-	public void execute(final Function<ContextInfo, List<Relation>> producer, String category, String prefix) throws Exception {
+	public void execute(final Function<ContextInfo, List<Relation>> producer, String category, String prefix)
+		throws Exception {
 
 		final Consumer<ContextInfo> consumer = ci -> producer.apply(ci).forEach(c -> writeEntity(c));
 
 		queryInformationSystem.getContextRelation(consumer, category, prefix);
 	}
 
-
 	protected void writeEntity(final Relation r) {
 		try {
 			writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r));

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpGraphEntities.java

@@ -11,8 +11,8 @@ import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.dump.oaf.*;
+import javax.swing.text.html.Option;
-import eu.dnetlib.dhp.schema.oaf.Journal;
+
 import org.apache.spark.SparkConf;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
@@ -26,12 +26,12 @@ import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
 import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.dump.oaf.*;
 import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
 import eu.dnetlib.dhp.schema.oaf.Field;
+import eu.dnetlib.dhp.schema.oaf.Journal;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
 
-import javax.swing.text.html.Option;
-
 public class DumpGraphEntities implements Serializable {
 
 	public void run(Boolean isSparkSessionManaged,
@@ -80,7 +80,8 @@ public class DumpGraphEntities implements Serializable {
 
 	}
 
-	private static <E extends OafEntity> void datasourceMap(SparkSession spark, String inputPath, String outputPath, Class<E> inputClazz) {
+	private static <E extends OafEntity> void datasourceMap(SparkSession spark, String inputPath, String outputPath,
+		Class<E> inputClazz) {
 		Utils
 			.readPath(spark, inputPath, inputClazz)
 			.map(d -> mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) d), Encoders.bean(Datasource.class))
@@ -90,8 +91,6 @@ public class DumpGraphEntities implements Serializable {
 			.json(outputPath);
 	}
 
-
-
 	private static <E extends OafEntity> void projectMap(SparkSession spark, String inputPath, String outputPath,
 		Class<E> inputClazz) {
 		Utils
@@ -110,83 +109,119 @@ public class DumpGraphEntities implements Serializable {
 
 		Optional.ofNullable(d.getOriginalId()).ifPresent(oId -> datasource.setOriginalId(oId));
 
-		Optional.ofNullable(d.getPid())
+		Optional
-				.ifPresent(pids -> pids.stream().map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
+			.ofNullable(d.getPid())
+			.ifPresent(
+				pids -> pids
+					.stream()
+					.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
 					.collect(Collectors.toList()));
 
-		Optional.ofNullable(d.getDatasourcetype())
+		Optional
-		.ifPresent(dsType -> datasource.setDatasourcetype(ControlledField.newInstance(dsType.getClassid(), dsType.getClassname())));
+			.ofNullable(d.getDatasourcetype())
+			.ifPresent(
+				dsType -> datasource
+					.setDatasourcetype(ControlledField.newInstance(dsType.getClassid(), dsType.getClassname())));
 
-		Optional.ofNullable(d.getOpenairecompatibility())
+		Optional
+			.ofNullable(d.getOpenairecompatibility())
 			.ifPresent(v -> datasource.setOpenairecompatibility(v.getClassname()));
 
-		Optional.ofNullable(d.getOfficialname())
+		Optional
+			.ofNullable(d.getOfficialname())
 			.ifPresent(oname -> datasource.setOfficialname(oname.getValue()));
 
-		Optional.ofNullable(d.getEnglishname())
+		Optional
+			.ofNullable(d.getEnglishname())
 			.ifPresent(ename -> datasource.setEnglishname(ename.getValue()));
 
-		Optional.ofNullable(d.getWebsiteurl())
+		Optional
+			.ofNullable(d.getWebsiteurl())
 			.ifPresent(wsite -> datasource.setWebsiteurl(wsite.getValue()));
 
-		Optional.ofNullable(d.getLogourl())
+		Optional
+			.ofNullable(d.getLogourl())
 			.ifPresent(lurl -> datasource.setLogourl(lurl.getValue()));
 
-		Optional.ofNullable(d.getDateofvalidation())
+		Optional
+			.ofNullable(d.getDateofvalidation())
 			.ifPresent(dval -> datasource.setDateofvalidation(dval.getValue()));
 
-		Optional.ofNullable(d.getDescription())
+		Optional
+			.ofNullable(d.getDescription())
 			.ifPresent(dex -> datasource.setDescription(dex.getValue()));
 
-		Optional.ofNullable(d.getSubjects())
+		Optional
-				.ifPresent(sbjs -> datasource.setSubjects(sbjs.stream().map(sbj -> sbj.getValue()).collect(Collectors.toList())));
+			.ofNullable(d.getSubjects())
+			.ifPresent(
+				sbjs -> datasource.setSubjects(sbjs.stream().map(sbj -> sbj.getValue()).collect(Collectors.toList())));
 
-		Optional.ofNullable(d.getOdpolicies())
+		Optional
+			.ofNullable(d.getOdpolicies())
 			.ifPresent(odp -> datasource.setPolicies(Arrays.asList(odp.getValue())));
 
-		Optional.ofNullable(d.getOdlanguages())
+		Optional
-				.ifPresent(langs -> datasource.setLanguages(langs.stream().map(lang -> lang.getValue()).collect(Collectors.toList())));
+			.ofNullable(d.getOdlanguages())
+			.ifPresent(
+				langs -> datasource
+					.setLanguages(langs.stream().map(lang -> lang.getValue()).collect(Collectors.toList())));
 
-		Optional.ofNullable(d.getOdcontenttypes())
+		Optional
-				.ifPresent(ctypes -> datasource.setContenttypes(ctypes.stream().map(ctype -> ctype.getValue()).collect(Collectors.toList())));
+			.ofNullable(d.getOdcontenttypes())
+			.ifPresent(
+				ctypes -> datasource
+					.setContenttypes(ctypes.stream().map(ctype -> ctype.getValue()).collect(Collectors.toList())));
 
-		Optional.ofNullable(d.getReleasestartdate())
+		Optional
+			.ofNullable(d.getReleasestartdate())
 			.ifPresent(rd -> datasource.setReleasestartdate(rd.getValue()));
 
-		Optional.ofNullable(d.getReleaseenddate())
+		Optional
+			.ofNullable(d.getReleaseenddate())
 			.ifPresent(ed -> datasource.setReleaseenddate(ed.getValue()));
 
-		Optional.ofNullable(d.getMissionstatementurl())
+		Optional
+			.ofNullable(d.getMissionstatementurl())
 			.ifPresent(ms -> datasource.setMissionstatementurl(ms.getValue()));
 
-		Optional.ofNullable(d.getDatabaseaccesstype())
+		Optional
+			.ofNullable(d.getDatabaseaccesstype())
 			.ifPresent(ar -> datasource.setAccessrights(ar.getValue()));
 
-		Optional.ofNullable(d.getDatauploadtype())
+		Optional
+			.ofNullable(d.getDatauploadtype())
 			.ifPresent(dut -> datasource.setUploadrights(dut.getValue()));
 
-		Optional.ofNullable(d.getDatabaseaccessrestriction())
+		Optional
+			.ofNullable(d.getDatabaseaccessrestriction())
 			.ifPresent(dar -> datasource.setDatabaseaccessrestriction(dar.getValue()));
 
-		Optional.ofNullable(d.getDatauploadrestriction())
+		Optional
+			.ofNullable(d.getDatauploadrestriction())
 			.ifPresent(dur -> datasource.setDatauploadrestriction(dur.getValue()));
 
-		Optional.ofNullable(d.getVersioning())
+		Optional
+			.ofNullable(d.getVersioning())
 			.ifPresent(v -> datasource.setVersioning(v.getValue()));
 
-		Optional.ofNullable(d.getCitationguidelineurl())
+		Optional
+			.ofNullable(d.getCitationguidelineurl())
 			.ifPresent(cu -> datasource.setCitationguidelineurl(cu.getValue()));
 
-		Optional.ofNullable(d.getPidsystems())
+		Optional
+			.ofNullable(d.getPidsystems())
 			.ifPresent(ps -> datasource.setPidsystems(ps.getValue()));
 
-		Optional.ofNullable(d.getCertificates())
+		Optional
+			.ofNullable(d.getCertificates())
 			.ifPresent(c -> datasource.setCertificates(c.getValue()));
 
-		Optional.ofNullable(d.getPolicies())
+		Optional
+			.ofNullable(d.getPolicies())
 			.ifPresent(ps -> datasource.setPolicies(ps.stream().map(p -> p.getValue()).collect(Collectors.toList())));
 
-		Optional.ofNullable(d.getJournal())
+		Optional
+			.ofNullable(d.getJournal())
 			.ifPresent(j -> datasource.setJournal(getContainer(j)));
 
 		return datasource;
@@ -196,37 +231,48 @@ public class DumpGraphEntities implements Serializable {
 	private static Container getContainer(Journal j) {
 		Container c = new Container();
 
-		Optional.ofNullable(j.getName())
+		Optional
+			.ofNullable(j.getName())
 			.ifPresent(n -> c.setName(n));
 
-		Optional.ofNullable(j.getIssnPrinted())
+		Optional
+			.ofNullable(j.getIssnPrinted())
 			.ifPresent(issnp -> c.setIssnPrinted(issnp));
 
-		Optional.ofNullable(j.getIssnOnline())
+		Optional
+			.ofNullable(j.getIssnOnline())
 			.ifPresent(issno -> c.setIssnOnline(issno));
 
-		Optional.ofNullable(j.getIssnLinking())
+		Optional
+			.ofNullable(j.getIssnLinking())
 			.ifPresent(isnl -> c.setIssnLinking(isnl));
 
-		Optional.ofNullable(j.getEp())
+		Optional
+			.ofNullable(j.getEp())
 			.ifPresent(ep -> c.setEp(ep));
 
-		Optional.ofNullable(j.getIss())
+		Optional
+			.ofNullable(j.getIss())
 			.ifPresent(iss -> c.setIss(iss));
 
-		Optional.ofNullable(j.getSp())
+		Optional
+			.ofNullable(j.getSp())
 			.ifPresent(sp -> c.setSp(sp));
 
-		Optional.ofNullable(j.getVol())
+		Optional
+			.ofNullable(j.getVol())
 			.ifPresent(vol -> c.setVol(vol));
 
-		Optional.ofNullable(j.getEdition())
+		Optional
+			.ofNullable(j.getEdition())
 			.ifPresent(edition -> c.setEdition(edition));
 
-		Optional.ofNullable(j.getConferencedate())
+		Optional
+			.ofNullable(j.getConferencedate())
 			.ifPresent(cdate -> c.setConferencedate(cdate));
 
-		Optional.ofNullable(j.getConferenceplace())
+		Optional
+			.ofNullable(j.getConferenceplace())
 			.ifPresent(cplace -> c.setConferenceplace(cplace));
 
 		return c;
@@ -466,8 +512,6 @@ public class DumpGraphEntities implements Serializable {
 							.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
 							.collect(Collectors.toList())));
 
-
-
 		return organization;
 	}
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Extractor.java

@@ -1,5 +1,17 @@
+
 package eu.dnetlib.dhp.oa.graph.dump.graph;
 
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.Serializable;
+import java.util.*;
+
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+
 import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
 import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
@@ -13,16 +25,6 @@ import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.Project;
 import eu.dnetlib.dhp.schema.oaf.Result;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.FlatMapFunction;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
-
-import java.io.Serializable;
-import java.util.*;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 public class Extractor implements Serializable {
 
@@ -43,8 +45,6 @@ public class Extractor implements Serializable {
 			});
 	}
 
-
-
 //    private static void extractRelationProjects(SparkSession spark, String inputPath, String outputPath){
 //        Utils.readPath(spark, inputPath, Project.class)
 //                .flatMap((FlatMapFunction<Project, Relation>) project ->{
@@ -70,7 +70,6 @@ public class Extractor implements Serializable {
 //                .json(outputPath);
 //    }
 
-
 	private <R extends Result> void extractRelationResult(SparkSession spark,
 		String inputPath,
 		String outputPath,
@@ -88,13 +87,15 @@ public class Extractor implements Serializable {
 					.ifPresent(inst -> inst.forEach(instance -> {
 						Optional
 							.ofNullable(instance.getCollectedfrom())
-                                        .ifPresent(cf ->
+							.ifPresent(
-                                                getRelatioPair(value, relationList, cf,
+								cf -> getRelatioPair(
-                                                        ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)
+									value, relationList, cf,
-                                        );
+									ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes));
 						Optional
 							.ofNullable(instance.getHostedby())
-                                        .ifPresent(hb -> getRelatioPair(value, relationList, hb,
+							.ifPresent(
+								hb -> getRelatioPair(
+									value, relationList, hb,
 									Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes));
 					}));
 				Set<String> communities = communityMap.keySet();

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Process.java

@@ -1,5 +1,10 @@
+
 package eu.dnetlib.dhp.oa.graph.dump.graph;
 
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
 import eu.dnetlib.dhp.oa.graph.dump.Constants;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
@@ -7,10 +12,6 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
 import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
 public class Process implements Serializable {
 
 	public static <R extends ResearchInitiative> R getEntity(ContextInfo ci) {

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/QueryInformationSystem.java

@@ -9,7 +9,6 @@ import java.util.*;
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.common.ModelSupport;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
 import org.dom4j.Element;
@@ -17,6 +16,7 @@ import org.dom4j.Node;
 import org.dom4j.io.SAXReader;
 import org.jetbrains.annotations.NotNull;
 
+import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkCollectAndSave.java

@@ -1,13 +1,12 @@
+
 package eu.dnetlib.dhp.oa.graph.dump.graph;
 
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
 import java.util.Optional;
 
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.oa.graph.dump.Utils;
-import eu.dnetlib.dhp.schema.dump.oaf.Result;
-import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.sql.SaveMode;
@@ -15,8 +14,10 @@ import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import eu.dnetlib.dhp.schema.dump.oaf.Result;
+import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
 
 public class SparkCollectAndSave implements Serializable {
 
@@ -55,11 +56,11 @@ public class SparkCollectAndSave implements Serializable {
 
 			});
 
-
 	}
 
 	private static void run(SparkSession spark, String inputPath, String outputPath) {
-        Utils.readPath(spark, inputPath + "/result/publication", Result.class)
+		Utils
+			.readPath(spark, inputPath + "/result/publication", Result.class)
 			.union(Utils.readPath(spark, inputPath + "/result/dataset", Result.class))
 			.union(Utils.readPath(spark, inputPath + "/result/otherresearchproduct", Result.class))
 			.union(Utils.readPath(spark, inputPath + "/result/software", Result.class))
@@ -68,7 +69,8 @@ public class SparkCollectAndSave implements Serializable {
 			.mode(SaveMode.Overwrite)
 			.json(outputPath);
 
-        Utils.readPath(spark, inputPath +"/relation/publication", Relation.class)
+		Utils
+			.readPath(spark, inputPath + "/relation/publication", Relation.class)
 			.union(Utils.readPath(spark, inputPath + "/relation/dataset", Relation.class))
 			.union(Utils.readPath(spark, inputPath + "/relation/orp", Relation.class))
 			.union(Utils.readPath(spark, inputPath + "/relation/software", Relation.class))

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkExtractRelationFromEntities.java

@@ -1,9 +1,9 @@
 
 package eu.dnetlib.dhp.oa.graph.dump.graph;
 
-
 import java.io.Serializable;
 import java.util.*;
+
 import org.apache.commons.io.IOUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -14,7 +14,6 @@ import eu.dnetlib.dhp.oa.graph.dump.Utils;
 import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
 import eu.dnetlib.dhp.schema.oaf.Result;
 
-
 public class SparkExtractRelationFromEntities implements Serializable {
 	private static final Logger log = LoggerFactory.getLogger(SparkExtractRelationFromEntities.class);
 
@@ -55,8 +54,6 @@ public class SparkExtractRelationFromEntities implements Serializable {
 		Extractor extractor = new Extractor();
 		extractor.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMap);
 
-
 	}
 
-
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkOrganizationRelation.java

@@ -1,34 +1,7 @@
+
 package eu.dnetlib.dhp.oa.graph.dump.graph;
 
-import com.google.gson.Gson;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-
-import eu.dnetlib.dhp.oa.graph.dump.Utils;
-
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
-import eu.dnetlib.dhp.schema.dump.oaf.graph.Node;
-import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType;
-import eu.dnetlib.dhp.schema.oaf.DataInfo;
-
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
-import org.apache.avro.generic.GenericData;
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FSDataOutputStream;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.spark.SparkConf;
-
-import org.apache.spark.api.java.JavaRDD;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.ForeachFunction;
-
-import org.apache.spark.sql.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import java.io.BufferedWriter;
 import java.io.IOException;
@@ -38,7 +11,31 @@ import java.nio.charset.StandardCharsets;
 import java.util.*;
 import java.util.concurrent.atomic.AtomicReference;
 
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import org.apache.avro.generic.GenericData;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.ForeachFunction;
+import org.apache.spark.sql.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.google.gson.Gson;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
+import eu.dnetlib.dhp.schema.dump.oaf.graph.Node;
+import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 
 public class SparkOrganizationRelation implements Serializable {
 	private static final Logger log = LoggerFactory.getLogger(SparkOrganizationRelation.class);
@@ -65,8 +62,8 @@ public class SparkOrganizationRelation implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
-
+		final OrganizationMap organizationMap = new Gson()
-        final OrganizationMap organizationMap = new Gson().fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class);
+			.fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class);
 		log.info("organization map : {}", new Gson().toJson(organizationMap));
 
 		SparkConf conf = new SparkConf();
@@ -83,7 +80,8 @@ public class SparkOrganizationRelation implements Serializable {
 
 	}
 
-    private static void writeRelations(SparkSession spark, Set<String> rels, String outputPath, OrganizationMap organizationMap) {
+	private static void writeRelations(SparkSession spark, Set<String> rels, String outputPath,
+		OrganizationMap organizationMap) {
 
 		List<eu.dnetlib.dhp.schema.dump.oaf.graph.Relation> relList = new ArrayList<>();
 
@@ -107,15 +105,14 @@ public class SparkOrganizationRelation implements Serializable {
 
 		});
 
-        spark.createDataset(relList, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class))
+		spark
+			.createDataset(relList, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
 			.json(outputPath);
 	}
 
-
-
 	private static Set<String> extractRelation(SparkSession spark, String inputPath, OrganizationMap organizationMap) {
 		Dataset<Relation> tmp = Utils.readPath(spark, inputPath, Relation.class);
 		Set<String> organizationSet = organizationMap.keySet();
@@ -133,13 +130,12 @@ public class SparkOrganizationRelation implements Serializable {
 						}
 					}
 				}
-        }});
+			}
+		});
 
 		toCreateRels.addAll(organizationSet);
 		return toCreateRels;
 
 	}
 
-
-
 }