Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop

dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_dnet.xml

@@ -19,7 +19,7 @@
         <setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration" value="do not insert"/>
         <setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws" value="do not insert"/>
         <setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement" value="common_lines"/>
-        <setting id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments" value="true"/>
+        <setting id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments" value="false"/>
         <setting id="org.eclipse.jdt.core.formatter.indentation.size" value="4"/>
         <setting id="org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator" value="do not insert"/>
         <setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration" value="common_lines"/>

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/MissingConceptDoiException.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.common.api;
 
 public class MissingConceptDoiException extends Throwable {

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java

@@ -12,14 +12,12 @@ import okhttp3.*;
 
 public class ZenodoAPIClient implements Serializable {
 
-
 	String urlString;
 	String bucket;
 
 	String deposition_id;
 	String access_token;
 
-
 	public static final MediaType MEDIA_TYPE_JSON = MediaType.parse("application/json; charset=utf-8");
 
 	private static final MediaType MEDIA_TYPE_ZIP = MediaType.parse("application/zip");
@@ -40,7 +38,9 @@ public class ZenodoAPIClient implements Serializable {
 		this.bucket = bucket;
 	}
 
-	public void setDeposition_id(String deposition_id){this.deposition_id = deposition_id;}
+	public void setDeposition_id(String deposition_id) {
+		this.deposition_id = deposition_id;
+	}
 
 	public ZenodoAPIClient(String urlString, String access_token) throws IOException {
 
@@ -205,8 +205,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(), ZenodoModelList.class);
 
-		for(ZenodoModel zm : zenodoModelList){
+		for (ZenodoModel zm : zenodoModelList) {
-			if (zm.getConceptrecid().equals(concept_rec_id)){
+			if (zm.getConceptrecid().equals(concept_rec_id)) {
 				deposition_id = zm.getId();
 				return;
 			}
@@ -255,12 +255,10 @@ public class ZenodoAPIClient implements Serializable {
 			// Get response body
 			ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class);
 
-
 			return zenodoModel.getLinks().getBucket();
 
 		}
 
 	}
 
-
 }

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModelList.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.common.api.zenodo;
 
 import java.util.ArrayList;

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Funder.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.schema.dump.oaf;
 
 import java.io.Serializable;

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Project.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.schema.dump.oaf;
 
 import java.io.Serializable;

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Organization.java

@@ -10,7 +10,6 @@ import eu.dnetlib.dhp.schema.dump.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.dump.oaf.Qualifier;
 import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
 
-
 /**
  * To represent the generic organizaiton. It has the following parameters:
  * - private String legalshortname to store the legalshortname of the organizaiton

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

@@ -368,7 +368,7 @@ public class ResultMapper implements Serializable {
 
 		Instance instance = new Instance();
 
-			if(!graph){
+		if (!graph) {
 			instance
 				.setCollectedfrom(
 					KeyValue
@@ -393,7 +393,6 @@ public class ResultMapper implements Serializable {
 			}
 		}
 
-
 		Optional
 			.ofNullable(i.getLicense())
 			.ifPresent(value -> instance.setLicense(value.getValue()));

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

@@ -3,11 +3,13 @@ package eu.dnetlib.dhp.oa.graph.dump;
 
 import java.io.Serializable;
 import java.util.Optional;
+
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.*;
+
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
 import eu.dnetlib.dhp.common.api.ZenodoAPIClient;

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

@@ -8,8 +8,6 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder;
-import eu.dnetlib.dhp.schema.dump.oaf.graph.Project;
 import org.apache.spark.SparkConf;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
@@ -24,6 +22,8 @@ import eu.dnetlib.dhp.oa.graph.dump.Utils;
 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.dump.oaf.graph.Funder;
+import eu.dnetlib.dhp.schema.dump.oaf.graph.Project;
 import eu.dnetlib.dhp.schema.oaf.Field;
 import eu.dnetlib.dhp.schema.oaf.Journal;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;

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

@@ -1,5 +1,4 @@
 
-
 package eu.dnetlib.dhp.oa.graph.dump.graph;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.graph.dump;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
@@ -16,7 +17,9 @@ import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+
 import com.fasterxml.jackson.databind.ObjectMapper;
+
 import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit;
 import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
 

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/ExtractRelationFromEntityTest.java

@@ -38,7 +38,6 @@ public class ExtractRelationFromEntityTest {
 	private static final Logger log = LoggerFactory
 		.getLogger(ExtractRelationFromEntityTest.class);
 
-
 	@BeforeAll
 	public static void beforeAll() throws IOException {
 		workingDir = Files